Starting phenix.real_space_refine on Sat Sep 28 19:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/09_2024/3j9j_5778.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/09_2024/3j9j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/09_2024/3j9j_5778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/09_2024/3j9j_5778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/09_2024/3j9j_5778.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/09_2024/3j9j_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.31, per 1000 atoms: 0.54 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: 5.80 Conformation dependent library (CDL) restraints added in 1.5 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: 1.32 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: 7.12 Time building geometry restraints manager: 6.84 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 2.010 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: 0.320 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.200 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.710 ------------------------------------------------------------------------------- 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= 0.947 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 524 time to evaluate : 1.599 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: 0.5290 time to fit residues: 378.5687 Evaluate side-chains 295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 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= 0.222 Angle : 0.604 4.742 14452 Z= 0.335 Chirality : 0.036 0.150 1624 Planarity : 0.005 0.069 1756 Dihedral : 4.190 21.643 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 *********************** 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 fitting. rotamer outliers: 30 poor density : 375 time to evaluate : 2.213 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: B 269 ILE cc_start: 0.6208 (mt) cc_final: 0.5705 (mt) outliers start: 30 outliers final: 15 residues processed: 383 average time/residue: 0.4556 time to fit residues: 247.9803 Evaluate side-chains 324 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 309 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS 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 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 62 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10700 Z= 0.256 Angle : 0.580 4.930 14452 Z= 0.324 Chirality : 0.036 0.132 1624 Planarity : 0.004 0.057 1756 Dihedral : 4.197 25.487 1408 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.59 % Favored : 93.77 % Rotamer: Outliers : 2.26 % Allowed : 12.67 % Favored : 85.07 % 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: 1.56 (0.23), residues: 1252 helix: 1.64 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 169 HIS 0.001 0.000 HIS C 30 PHE 0.015 0.001 PHE B 252 TYR 0.010 0.001 TYR C 185 ARG 0.002 0.000 ARG D 177 *********************** 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 356 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 330 time to evaluate : 1.648 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: A 204 TYR cc_start: 0.6181 (t80) cc_final: 0.5834 (t80) REVERT: B 204 TYR cc_start: 0.6220 (t80) cc_final: 0.5862 (t80) REVERT: C 204 TYR cc_start: 0.6200 (t80) cc_final: 0.5957 (t80) REVERT: D 204 TYR cc_start: 0.6218 (t80) cc_final: 0.5885 (t80) outliers start: 26 outliers final: 20 residues processed: 333 average time/residue: 0.4630 time to fit residues: 219.3307 Evaluate side-chains 319 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 299 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 181 GLN 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 181 GLN 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 192 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 218 LEU 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 111 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6011 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10700 Z= 0.224 Angle : 0.544 4.029 14452 Z= 0.302 Chirality : 0.035 0.133 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.167 26.106 1408 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.75 % Favored : 93.61 % Rotamer: Outliers : 2.43 % Allowed : 15.54 % Favored : 82.03 % 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: 1.82 (0.24), residues: 1252 helix: 1.84 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.03 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 294 HIS 0.000 0.000 HIS A 30 PHE 0.012 0.001 PHE B 179 TYR 0.009 0.001 TYR C 185 ARG 0.002 0.000 ARG C 177 *********************** 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 355 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 327 time to evaluate : 1.783 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: A 204 TYR cc_start: 0.6233 (t80) cc_final: 0.5841 (t80) REVERT: B 204 TYR cc_start: 0.6219 (t80) cc_final: 0.5855 (t80) REVERT: C 204 TYR cc_start: 0.6229 (t80) cc_final: 0.5888 (t80) REVERT: D 204 TYR cc_start: 0.6241 (t80) cc_final: 0.5870 (t80) outliers start: 28 outliers final: 17 residues processed: 332 average time/residue: 0.4620 time to fit residues: 222.3217 Evaluate side-chains 316 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 299 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU 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 C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10700 Z= 0.291 Angle : 0.568 5.048 14452 Z= 0.320 Chirality : 0.036 0.149 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.298 27.495 1408 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.13 % Rotamer: Outliers : 1.82 % Allowed : 17.80 % Favored : 80.38 % 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: 1.74 (0.24), residues: 1252 helix: 1.81 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.19 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 294 HIS 0.002 0.001 HIS A 30 PHE 0.011 0.001 PHE B 211 TYR 0.010 0.001 TYR C 61 ARG 0.003 0.000 ARG D 177 *********************** 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 334 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 313 time to evaluate : 1.504 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: A 241 MET cc_start: 0.5915 (mmp) cc_final: 0.5675 (mmt) outliers start: 21 outliers final: 17 residues processed: 314 average time/residue: 0.4438 time to fit residues: 200.8240 Evaluate side-chains 307 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 290 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU 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 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 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 261 LEU 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 40 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10700 Z= 0.226 Angle : 0.534 4.477 14452 Z= 0.298 Chirality : 0.036 0.160 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.231 28.213 1408 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.79 % Favored : 92.89 % Rotamer: Outliers : 2.26 % Allowed : 17.45 % Favored : 80.30 % 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: 1.89 (0.24), residues: 1252 helix: 1.94 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 294 HIS 0.001 0.000 HIS C 30 PHE 0.010 0.001 PHE D 211 TYR 0.015 0.001 TYR A 185 ARG 0.003 0.000 ARG D 29 *********************** 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 334 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 308 time to evaluate : 1.759 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 outliers start: 26 outliers final: 16 residues processed: 310 average time/residue: 0.4395 time to fit residues: 198.8361 Evaluate side-chains 304 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 288 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 190 GLU 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 C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 261 LEU 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 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10700 Z= 0.257 Angle : 0.561 5.862 14452 Z= 0.312 Chirality : 0.035 0.135 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.219 28.619 1408 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.13 % Rotamer: Outliers : 2.69 % Allowed : 18.92 % Favored : 78.39 % 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: 1.88 (0.24), residues: 1252 helix: 1.97 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 169 HIS 0.001 0.001 HIS B 30 PHE 0.010 0.001 PHE B 68 TYR 0.010 0.001 TYR B 61 ARG 0.003 0.000 ARG C 177 *********************** 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 324 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 293 time to evaluate : 1.569 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: A 241 MET cc_start: 0.6214 (mmt) cc_final: 0.5882 (mmt) outliers start: 31 outliers final: 17 residues processed: 300 average time/residue: 0.4223 time to fit residues: 185.0259 Evaluate side-chains 300 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 283 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.7215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10700 Z= 0.232 Angle : 0.557 4.828 14452 Z= 0.309 Chirality : 0.037 0.174 1624 Planarity : 0.004 0.053 1756 Dihedral : 4.220 27.789 1408 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.03 % Favored : 92.65 % Rotamer: Outliers : 2.17 % Allowed : 20.14 % Favored : 77.69 % 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: 1.92 (0.24), residues: 1252 helix: 2.05 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 169 HIS 0.001 0.000 HIS C 30 PHE 0.011 0.001 PHE A 202 TYR 0.011 0.001 TYR D 185 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 8 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 314 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 289 time to evaluate : 1.649 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: A 241 MET cc_start: 0.6182 (mmp) cc_final: 0.5728 (mmt) outliers start: 25 outliers final: 15 residues processed: 293 average time/residue: 0.4303 time to fit residues: 183.5605 Evaluate side-chains 287 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 272 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 114 GLN Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 281 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10700 Z= 0.192 Angle : 0.562 7.493 14452 Z= 0.303 Chirality : 0.036 0.158 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.165 26.248 1408 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.63 % Favored : 93.05 % Rotamer: Outliers : 2.26 % Allowed : 20.14 % Favored : 77.60 % 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: 2.12 (0.24), residues: 1252 helix: 2.17 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 294 HIS 0.001 0.000 HIS A 30 PHE 0.011 0.001 PHE A 202 TYR 0.015 0.001 TYR D 185 ARG 0.002 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 9 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 312 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 286 time to evaluate : 1.724 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: A 241 MET cc_start: 0.6067 (mmp) cc_final: 0.5548 (mmt) REVERT: B 204 TYR cc_start: 0.6248 (t80) cc_final: 0.5836 (t80) outliers start: 26 outliers final: 15 residues processed: 291 average time/residue: 0.4379 time to fit residues: 185.8674 Evaluate side-chains 293 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain D residue 113 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.7475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10700 Z= 0.311 Angle : 0.595 4.872 14452 Z= 0.334 Chirality : 0.038 0.143 1624 Planarity : 0.004 0.051 1756 Dihedral : 4.267 28.529 1408 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.03 % Favored : 92.65 % Rotamer: Outliers : 1.74 % Allowed : 20.75 % Favored : 77.52 % 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: 1.82 (0.24), residues: 1252 helix: 1.94 (0.16), residues: 976 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 169 HIS 0.001 0.001 HIS B 30 PHE 0.012 0.001 PHE A 202 TYR 0.014 0.002 TYR D 185 ARG 0.003 0.000 ARG D 177 ********************** REFINEMENT MACRO_CYCLE 10 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 300 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 280 time to evaluate : 1.655 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: A 241 MET cc_start: 0.6213 (mmp) cc_final: 0.5865 (mmt) outliers start: 20 outliers final: 10 residues processed: 283 average time/residue: 0.4227 time to fit residues: 174.0963 Evaluate side-chains 285 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 275 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 281 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.082525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070608 restraints weight = 109625.548| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.37 r_work: 0.3085 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10700 Z= 0.175 Angle : 0.586 9.323 14452 Z= 0.310 Chirality : 0.037 0.170 1624 Planarity : 0.004 0.054 1756 Dihedral : 4.131 24.924 1408 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.87 % Favored : 92.81 % Rotamer: Outliers : 1.56 % Allowed : 21.35 % Favored : 77.08 % 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: 2.16 (0.24), residues: 1252 helix: 2.15 (0.16), residues: 976 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 169 HIS 0.000 0.000 HIS C 30 PHE 0.012 0.001 PHE D 202 TYR 0.012 0.001 TYR D 185 ARG 0.003 0.000 ARG A 314 =============================================================================== Job complete usr+sys time: 5240.34 seconds wall clock time: 91 minutes 37.46 seconds (5497.46 seconds total)