Starting phenix.real_space_refine on Tue Sep 24 06:00:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/09_2024/6u5h_20646.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/09_2024/6u5h_20646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/09_2024/6u5h_20646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/09_2024/6u5h_20646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/09_2024/6u5h_20646.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/09_2024/6u5h_20646.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4530 2.51 5 N 1362 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7326 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2442 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: C, B Time building chain proxies: 4.32, per 1000 atoms: 0.59 Number of scatterers: 7326 At special positions: 0 Unit cell: (90.567, 94.731, 78.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1392 8.00 N 1362 7.00 C 4530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 931.8 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 10.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 177' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 177 " --> pdb=" O PRO B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 177' Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.753A pdb=" N ASP A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.610A pdb=" N GLU A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.994A pdb=" N ARG A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 8 removed outlier: 3.668A pdb=" N GLY C 63 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 73 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 62 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG C 71 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG C 41 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU C 25 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR C 39 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191 removed outlier: 5.676A pdb=" N ILE C 303 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN C 322 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY B 63 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 73 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 62 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG B 71 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG B 41 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 25 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 39 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE B 303 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 322 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY A 63 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 73 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 62 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG A 71 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG A 41 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 25 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR A 39 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE A 303 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN A 322 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 202 through 203 81 hydrogen bonds defined for protein. 225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2539 1.34 - 1.46: 1375 1.46 - 1.58: 3460 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 7443 Sorted by residual: bond pdb=" C LEU A 218 " pdb=" N PRO A 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.76e+00 bond pdb=" CB PRO A 86 " pdb=" CG PRO A 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.76e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" CB PRO C 86 " pdb=" CG PRO C 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" C LEU B 218 " pdb=" N PRO B 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.66e+00 ... (remaining 7438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 9573 2.10 - 4.20: 387 4.20 - 6.30: 48 6.30 - 8.39: 26 8.39 - 10.49: 19 Bond angle restraints: 10053 Sorted by residual: angle pdb=" N VAL B 14 " pdb=" CA VAL B 14 " pdb=" C VAL B 14 " ideal model delta sigma weight residual 108.95 101.03 7.92 1.65e+00 3.67e-01 2.31e+01 angle pdb=" N VAL A 14 " pdb=" CA VAL A 14 " pdb=" C VAL A 14 " ideal model delta sigma weight residual 108.95 101.07 7.88 1.65e+00 3.67e-01 2.28e+01 angle pdb=" N VAL C 14 " pdb=" CA VAL C 14 " pdb=" C VAL C 14 " ideal model delta sigma weight residual 108.95 101.09 7.86 1.65e+00 3.67e-01 2.27e+01 angle pdb=" CA PRO A 85 " pdb=" C PRO A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 117.93 123.03 -5.10 1.20e+00 6.94e-01 1.81e+01 angle pdb=" CA PRO B 85 " pdb=" C PRO B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 117.93 123.00 -5.07 1.20e+00 6.94e-01 1.78e+01 ... (remaining 10048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 4254 14.28 - 28.55: 249 28.55 - 42.83: 9 42.83 - 57.10: 0 57.10 - 71.38: 6 Dihedral angle restraints: 4518 sinusoidal: 1830 harmonic: 2688 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N ASP B 200 " pdb=" CA ASP B 200 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE A 199 " pdb=" C PHE A 199 " pdb=" N ASP A 200 " pdb=" CA ASP A 200 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PHE C 199 " pdb=" C PHE C 199 " pdb=" N ASP C 200 " pdb=" CA ASP C 200 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 4515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 824 0.058 - 0.117: 229 0.117 - 0.175: 61 0.175 - 0.233: 8 0.233 - 0.292: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE B 105 " pdb=" CA ILE B 105 " pdb=" CG1 ILE B 105 " pdb=" CG2 ILE B 105 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1122 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 187 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 187 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " 0.035 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1109 2.77 - 3.30: 6094 3.30 - 3.83: 11304 3.83 - 4.37: 13014 4.37 - 4.90: 22207 Nonbonded interactions: 53728 Sorted by model distance: nonbonded pdb=" OG1 THR B 79 " pdb=" OG1 THR B 92 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR C 79 " pdb=" OG1 THR C 92 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 79 " pdb=" OG1 THR A 92 " model vdw 2.234 3.040 nonbonded pdb=" O THR B 104 " pdb=" OG1 THR B 153 " model vdw 2.246 3.040 nonbonded pdb=" O THR C 104 " pdb=" OG1 THR C 153 " model vdw 2.247 3.040 ... (remaining 53723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.660 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7443 Z= 0.355 Angle : 1.067 10.493 10053 Z= 0.571 Chirality : 0.059 0.292 1125 Planarity : 0.006 0.063 1326 Dihedral : 8.739 71.380 2796 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.22), residues: 942 helix: -5.41 (0.09), residues: 90 sheet: -3.34 (0.32), residues: 213 loop : -3.43 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 315 HIS 0.006 0.002 HIS C 150 PHE 0.011 0.002 PHE A 151 TYR 0.023 0.002 TYR C 310 ARG 0.006 0.001 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8442 (p) cc_final: 0.8184 (p) REVERT: C 198 SER cc_start: 0.8614 (p) cc_final: 0.8385 (m) REVERT: C 215 ARG cc_start: 0.6463 (mtt180) cc_final: 0.5761 (mmm160) REVERT: B 44 ASP cc_start: 0.8156 (m-30) cc_final: 0.7889 (m-30) REVERT: B 48 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7931 (mm-40) REVERT: B 64 TYR cc_start: 0.8561 (m-10) cc_final: 0.8121 (m-10) REVERT: B 215 ARG cc_start: 0.6355 (mtt180) cc_final: 0.5448 (mmm160) REVERT: B 289 LEU cc_start: 0.7809 (mt) cc_final: 0.7508 (mt) REVERT: A 205 ASP cc_start: 0.7634 (m-30) cc_final: 0.7286 (m-30) REVERT: A 215 ARG cc_start: 0.6525 (mtt180) cc_final: 0.5844 (mmp-170) REVERT: A 281 ASP cc_start: 0.7677 (m-30) cc_final: 0.7103 (m-30) outliers start: 3 outliers final: 0 residues processed: 226 average time/residue: 0.2720 time to fit residues: 75.1199 Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS B 81 GLN B 242 HIS A 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7443 Z= 0.282 Angle : 0.769 7.440 10053 Z= 0.392 Chirality : 0.047 0.134 1125 Planarity : 0.006 0.048 1326 Dihedral : 7.189 25.760 1059 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.22 % Allowed : 7.98 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.22), residues: 942 helix: -5.13 (0.18), residues: 96 sheet: -3.57 (0.26), residues: 267 loop : -3.08 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 315 HIS 0.003 0.001 HIS A 246 PHE 0.015 0.002 PHE C 265 TYR 0.020 0.002 TYR A 159 ARG 0.004 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7373 (mtt180) cc_final: 0.7120 (mmt90) REVERT: C 205 ASP cc_start: 0.7921 (m-30) cc_final: 0.7587 (m-30) REVERT: C 215 ARG cc_start: 0.6538 (mtt180) cc_final: 0.5769 (mmm160) REVERT: C 322 ASN cc_start: 0.7186 (m110) cc_final: 0.6755 (m110) REVERT: B 215 ARG cc_start: 0.6202 (mtt180) cc_final: 0.5290 (mmm160) REVERT: B 302 LEU cc_start: 0.8502 (mt) cc_final: 0.8164 (mt) REVERT: B 322 ASN cc_start: 0.6951 (m110) cc_final: 0.6522 (m110) REVERT: A 120 ARG cc_start: 0.7146 (mtt90) cc_final: 0.6563 (mmt90) REVERT: A 205 ASP cc_start: 0.7758 (m-30) cc_final: 0.7243 (m-30) REVERT: A 215 ARG cc_start: 0.6640 (mtt180) cc_final: 0.5813 (mmm160) REVERT: A 259 LYS cc_start: 0.5888 (mttt) cc_final: 0.5486 (mmtp) outliers start: 25 outliers final: 19 residues processed: 171 average time/residue: 0.2370 time to fit residues: 51.6148 Evaluate side-chains 156 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 75 optimal weight: 50.0000 chunk 83 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 HIS A 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7443 Z= 0.360 Angle : 0.799 9.185 10053 Z= 0.406 Chirality : 0.048 0.140 1125 Planarity : 0.006 0.049 1326 Dihedral : 7.110 26.675 1059 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 3.47 % Allowed : 12.10 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.23), residues: 942 helix: -4.92 (0.22), residues: 114 sheet: -3.46 (0.28), residues: 273 loop : -2.98 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 315 HIS 0.004 0.001 HIS A 246 PHE 0.020 0.002 PHE B 265 TYR 0.016 0.002 TYR B 159 ARG 0.005 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7126 (mmt90) REVERT: C 215 ARG cc_start: 0.6425 (mtt180) cc_final: 0.5506 (mmm160) REVERT: C 322 ASN cc_start: 0.7146 (m110) cc_final: 0.6593 (m110) REVERT: B 1 MET cc_start: 0.7110 (mmp) cc_final: 0.6841 (mmm) REVERT: B 15 THR cc_start: 0.7827 (t) cc_final: 0.7595 (p) REVERT: B 215 ARG cc_start: 0.6272 (mtt180) cc_final: 0.5285 (mmm160) REVERT: B 310 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: A 120 ARG cc_start: 0.7271 (mtt90) cc_final: 0.6962 (mtt90) REVERT: A 205 ASP cc_start: 0.7862 (m-30) cc_final: 0.7265 (m-30) REVERT: A 215 ARG cc_start: 0.6604 (mtt180) cc_final: 0.5662 (mmm160) REVERT: A 259 LYS cc_start: 0.5895 (mttt) cc_final: 0.5509 (mmtt) REVERT: A 322 ASN cc_start: 0.7182 (m110) cc_final: 0.6865 (m-40) outliers start: 27 outliers final: 23 residues processed: 160 average time/residue: 0.2454 time to fit residues: 49.2783 Evaluate side-chains 157 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7443 Z= 0.317 Angle : 0.754 9.551 10053 Z= 0.382 Chirality : 0.047 0.139 1125 Planarity : 0.006 0.047 1326 Dihedral : 6.847 25.831 1059 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer: Outliers : 4.25 % Allowed : 13.77 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.22), residues: 942 helix: -5.02 (0.17), residues: 114 sheet: -3.44 (0.27), residues: 297 loop : -2.99 (0.22), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 82 HIS 0.003 0.001 HIS B 246 PHE 0.027 0.002 PHE B 265 TYR 0.010 0.002 TYR C 310 ARG 0.006 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 215 ARG cc_start: 0.6602 (mtt180) cc_final: 0.5740 (mmm160) REVERT: C 322 ASN cc_start: 0.7121 (m110) cc_final: 0.6826 (m110) REVERT: B 157 ARG cc_start: 0.4015 (mmm160) cc_final: 0.3797 (mmm160) REVERT: B 169 MET cc_start: 0.2764 (mmt) cc_final: 0.2364 (mmt) REVERT: B 310 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6620 (m-10) REVERT: A 215 ARG cc_start: 0.6740 (mtt180) cc_final: 0.5629 (mmm160) REVERT: A 259 LYS cc_start: 0.6028 (mttt) cc_final: 0.5623 (mmtt) REVERT: A 322 ASN cc_start: 0.7298 (m110) cc_final: 0.6996 (m-40) outliers start: 33 outliers final: 26 residues processed: 156 average time/residue: 0.2504 time to fit residues: 49.7205 Evaluate side-chains 152 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7443 Z= 0.332 Angle : 0.750 9.526 10053 Z= 0.380 Chirality : 0.047 0.144 1125 Planarity : 0.006 0.048 1326 Dihedral : 6.749 25.408 1059 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 5.15 % Allowed : 13.90 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.23), residues: 942 helix: -5.02 (0.15), residues: 120 sheet: -3.47 (0.27), residues: 297 loop : -2.94 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 315 HIS 0.002 0.001 HIS B 246 PHE 0.018 0.002 PHE A 265 TYR 0.017 0.002 TYR B 216 ARG 0.008 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 322 ASN cc_start: 0.7116 (m110) cc_final: 0.6823 (m110) REVERT: B 169 MET cc_start: 0.2854 (mmt) cc_final: 0.2545 (mmt) REVERT: B 294 LYS cc_start: 0.5137 (OUTLIER) cc_final: 0.4673 (mtmt) REVERT: B 310 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6618 (m-10) REVERT: A 120 ARG cc_start: 0.7291 (mtt90) cc_final: 0.6731 (mtm180) REVERT: A 215 ARG cc_start: 0.6665 (mtt180) cc_final: 0.5578 (mmm160) REVERT: A 230 LYS cc_start: 0.3780 (mttt) cc_final: 0.3308 (tptp) REVERT: A 259 LYS cc_start: 0.6042 (mttt) cc_final: 0.5579 (mmmt) REVERT: A 294 LYS cc_start: 0.4671 (OUTLIER) cc_final: 0.4080 (mtpt) REVERT: A 322 ASN cc_start: 0.7312 (m110) cc_final: 0.6565 (m110) outliers start: 40 outliers final: 27 residues processed: 150 average time/residue: 0.2539 time to fit residues: 47.8172 Evaluate side-chains 152 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 294 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 7.9990 chunk 80 optimal weight: 0.0870 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 40.0000 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 4.1764 ------------------------------------------------------------------------------- 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: 0.7047 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7443 Z= 0.263 Angle : 0.701 7.695 10053 Z= 0.354 Chirality : 0.046 0.177 1125 Planarity : 0.005 0.043 1326 Dihedral : 6.443 25.519 1059 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 4.63 % Allowed : 15.70 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.23), residues: 942 helix: -5.04 (0.14), residues: 120 sheet: -3.39 (0.27), residues: 297 loop : -2.93 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 315 HIS 0.002 0.001 HIS B 246 PHE 0.017 0.001 PHE A 265 TYR 0.008 0.001 TYR B 310 ARG 0.011 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7467 (mtt90) cc_final: 0.7252 (mtt180) REVERT: C 304 ASP cc_start: 0.8379 (m-30) cc_final: 0.8010 (m-30) REVERT: C 322 ASN cc_start: 0.7052 (m110) cc_final: 0.6842 (m110) REVERT: B 48 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7837 (mm-40) REVERT: B 199 PHE cc_start: 0.7568 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: B 310 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: A 215 ARG cc_start: 0.6613 (mtt180) cc_final: 0.5504 (mmm160) REVERT: A 230 LYS cc_start: 0.3649 (mttt) cc_final: 0.3306 (tptp) REVERT: A 259 LYS cc_start: 0.5983 (mttt) cc_final: 0.5569 (mmtp) outliers start: 36 outliers final: 28 residues processed: 148 average time/residue: 0.2587 time to fit residues: 48.0737 Evaluate side-chains 152 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 30.0000 chunk 10 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7443 Z= 0.346 Angle : 0.745 8.740 10053 Z= 0.378 Chirality : 0.047 0.172 1125 Planarity : 0.006 0.045 1326 Dihedral : 6.603 25.693 1059 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.39 % Favored : 84.61 % Rotamer: Outliers : 5.79 % Allowed : 15.83 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.23), residues: 942 helix: -5.15 (0.12), residues: 129 sheet: -3.47 (0.27), residues: 297 loop : -3.01 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 315 HIS 0.003 0.001 HIS B 246 PHE 0.016 0.002 PHE A 265 TYR 0.010 0.002 TYR B 159 ARG 0.010 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7350 (mtt90) cc_final: 0.7079 (mtt180) REVERT: C 230 LYS cc_start: 0.3728 (mttt) cc_final: 0.3153 (tppp) REVERT: B 48 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7831 (mm-40) REVERT: B 120 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7098 (mpt180) REVERT: B 169 MET cc_start: 0.2951 (mmt) cc_final: 0.2688 (mmt) REVERT: B 209 MET cc_start: 0.7202 (mtt) cc_final: 0.6849 (mtt) REVERT: B 310 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.6693 (m-10) REVERT: A 215 ARG cc_start: 0.6601 (mtt180) cc_final: 0.5504 (mmm160) REVERT: A 251 ARG cc_start: 0.1765 (mtt180) cc_final: 0.0326 (mtm-85) REVERT: A 259 LYS cc_start: 0.6036 (mttt) cc_final: 0.5586 (mmtp) outliers start: 45 outliers final: 34 residues processed: 158 average time/residue: 0.2558 time to fit residues: 50.6498 Evaluate side-chains 156 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 10.0000 chunk 53 optimal weight: 0.0170 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 overall best weight: 0.4824 ------------------------------------------------------------------------------- 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: 0.6975 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7443 Z= 0.168 Angle : 0.671 9.478 10053 Z= 0.332 Chirality : 0.045 0.170 1125 Planarity : 0.004 0.036 1326 Dihedral : 5.913 22.495 1059 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 3.09 % Allowed : 19.43 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.23), residues: 942 helix: -4.99 (0.14), residues: 123 sheet: -2.85 (0.29), residues: 282 loop : -2.95 (0.23), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.003 0.001 HIS A 150 PHE 0.013 0.001 PHE A 293 TYR 0.011 0.001 TYR A 216 ARG 0.011 0.000 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 LEU cc_start: 0.8438 (mt) cc_final: 0.8205 (mt) REVERT: C 120 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6836 (mtt180) REVERT: C 138 ILE cc_start: 0.4974 (mt) cc_final: 0.4617 (mt) REVERT: B 120 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7230 (mpt180) REVERT: B 157 ARG cc_start: 0.3832 (mmm160) cc_final: 0.3621 (mmm160) REVERT: B 310 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6378 (m-10) REVERT: B 322 ASN cc_start: 0.7373 (m110) cc_final: 0.7016 (m110) REVERT: A 1 MET cc_start: 0.7242 (mmp) cc_final: 0.6841 (mmp) REVERT: A 215 ARG cc_start: 0.6696 (mtt180) cc_final: 0.5659 (mmm160) REVERT: A 259 LYS cc_start: 0.5919 (mttt) cc_final: 0.5543 (mmtp) outliers start: 24 outliers final: 19 residues processed: 154 average time/residue: 0.2587 time to fit residues: 49.2727 Evaluate side-chains 144 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN B 81 GLN A 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7443 Z= 0.341 Angle : 0.738 9.045 10053 Z= 0.373 Chirality : 0.047 0.171 1125 Planarity : 0.006 0.045 1326 Dihedral : 6.406 23.853 1059 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.39 % Favored : 84.61 % Rotamer: Outliers : 3.60 % Allowed : 19.05 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.23), residues: 942 helix: -4.98 (0.15), residues: 123 sheet: -3.25 (0.27), residues: 309 loop : -2.99 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 315 HIS 0.003 0.001 HIS B 246 PHE 0.014 0.002 PHE B 265 TYR 0.012 0.002 TYR C 159 ARG 0.006 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7317 (mtt90) cc_final: 0.7023 (mtt180) REVERT: B 120 ARG cc_start: 0.7716 (mmt180) cc_final: 0.7411 (mpt180) REVERT: B 310 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.6692 (m-10) REVERT: A 82 TRP cc_start: 0.8829 (OUTLIER) cc_final: 0.8522 (m100) REVERT: A 157 ARG cc_start: 0.4550 (mmm160) cc_final: 0.4147 (mmm160) REVERT: A 215 ARG cc_start: 0.6665 (mtt180) cc_final: 0.5542 (mmm160) REVERT: A 259 LYS cc_start: 0.5997 (mttt) cc_final: 0.5591 (mmtp) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.2849 time to fit residues: 49.2693 Evaluate side-chains 146 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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: 0.7083 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7443 Z= 0.261 Angle : 0.703 9.450 10053 Z= 0.353 Chirality : 0.046 0.166 1125 Planarity : 0.006 0.066 1326 Dihedral : 6.248 24.098 1059 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 3.35 % Allowed : 19.56 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.23), residues: 942 helix: -4.57 (0.22), residues: 138 sheet: -2.94 (0.31), residues: 264 loop : -3.09 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 315 HIS 0.003 0.001 HIS B 246 PHE 0.012 0.001 PHE B 265 TYR 0.008 0.001 TYR C 159 ARG 0.014 0.001 ARG B 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7256 (mpt180) REVERT: B 210 ARG cc_start: 0.6089 (mmt-90) cc_final: 0.5020 (tpp-160) REVERT: B 310 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6545 (m-10) REVERT: A 82 TRP cc_start: 0.8817 (OUTLIER) cc_final: 0.8483 (m100) REVERT: A 259 LYS cc_start: 0.5972 (mttt) cc_final: 0.5569 (mmtp) outliers start: 26 outliers final: 21 residues processed: 139 average time/residue: 0.2683 time to fit residues: 46.2924 Evaluate side-chains 141 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.0020 chunk 68 optimal weight: 8.9990 chunk 10 optimal weight: 40.0000 chunk 20 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 0.0030 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 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 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.222215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.187355 restraints weight = 7907.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.187305 restraints weight = 11393.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.186043 restraints weight = 10373.856| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7443 Z= 0.164 Angle : 0.648 8.997 10053 Z= 0.324 Chirality : 0.045 0.161 1125 Planarity : 0.004 0.051 1326 Dihedral : 5.651 19.371 1059 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 2.83 % Allowed : 19.56 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.24), residues: 942 helix: -4.80 (0.19), residues: 132 sheet: -2.42 (0.31), residues: 288 loop : -2.86 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.002 0.001 HIS C 150 PHE 0.010 0.001 PHE A 265 TYR 0.005 0.001 TYR A 159 ARG 0.013 0.000 ARG B 157 =============================================================================== Job complete usr+sys time: 1724.39 seconds wall clock time: 31 minutes 31.06 seconds (1891.06 seconds total)