Starting phenix.real_space_refine on Fri Dec 27 11:07:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v0y_26953/12_2024/7v0y_26953.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v0y_26953/12_2024/7v0y_26953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v0y_26953/12_2024/7v0y_26953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v0y_26953/12_2024/7v0y_26953.map" model { file = "/net/cci-nas-00/data/ceres_data/7v0y_26953/12_2024/7v0y_26953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v0y_26953/12_2024/7v0y_26953.cif" } resolution = 3.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.239 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 12 5.16 5 C 2840 2.51 5 N 777 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4454 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2270 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2183 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.77, per 1000 atoms: 0.85 Number of scatterers: 4454 At special positions: 0 Unit cell: (93.375, 75.53, 64.325, 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 12 16.00 O 825 8.00 N 777 7.00 C 2840 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: 1.06 Conformation dependent library (CDL) restraints added in 633.8 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 40.9% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.765A pdb=" N LYS E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 165 through 170 removed outlier: 4.262A pdb=" N ALA E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 200 Processing helix chain 'E' and resid 277 through 291 Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.765A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 349 Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.668A pdb=" N LYS C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 277 through 291 Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.748A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.439A pdb=" N VAL C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 85 through 87 removed outlier: 6.737A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 123 removed outlier: 6.423A pdb=" N THR E 118 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ARG E 246 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU E 120 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN E 248 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP E 122 " --> pdb=" O GLN E 248 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N ALA E 250 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG E 263 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA E 226 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 264 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR E 58 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL E 229 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU E 60 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL E 231 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN E 62 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ARG E 233 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU E 64 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 87 removed outlier: 6.862A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS C 56 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR C 227 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR C 58 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL C 229 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU C 60 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL C 231 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN C 62 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE C 262 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA C 226 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 264 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG C 263 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C 248 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 87 removed outlier: 6.862A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 582 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: 1.32 Time building geometry restraints manager: 1.24 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: 1517 1.34 - 1.46: 832 1.46 - 1.58: 2173 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4542 Sorted by residual: bond pdb=" C VAL E 336 " pdb=" N PRO E 337 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.28e-02 6.10e+03 6.13e+00 bond pdb=" CB GLN E 302 " pdb=" CG GLN E 302 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB ASN C 91 " pdb=" CG ASN C 91 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CG GLN E 302 " pdb=" CD GLN E 302 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.39e-01 bond pdb=" N ASN C 91 " pdb=" CA ASN C 91 " ideal model delta sigma weight residual 1.458 1.474 -0.016 1.77e-02 3.19e+03 7.74e-01 ... (remaining 4537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 5966 1.51 - 3.02: 161 3.02 - 4.53: 27 4.53 - 6.04: 7 6.04 - 7.56: 3 Bond angle restraints: 6164 Sorted by residual: angle pdb=" C SER E 328 " pdb=" N GLU E 329 " pdb=" CA GLU E 329 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C GLU C 90 " pdb=" N ASN C 91 " pdb=" CA ASN C 91 " ideal model delta sigma weight residual 125.66 131.25 -5.59 1.85e+00 2.92e-01 9.12e+00 angle pdb=" CB GLN E 302 " pdb=" CG GLN E 302 " pdb=" CD GLN E 302 " ideal model delta sigma weight residual 112.60 117.33 -4.73 1.70e+00 3.46e-01 7.73e+00 angle pdb=" C VAL E 82 " pdb=" N GLN E 83 " pdb=" CA GLN E 83 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.45e+00 angle pdb=" N ASP E 277 " pdb=" CA ASP E 277 " pdb=" C ASP E 277 " ideal model delta sigma weight residual 108.52 104.93 3.59 1.63e+00 3.76e-01 4.85e+00 ... (remaining 6159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 2332 16.85 - 33.71: 262 33.71 - 50.56: 116 50.56 - 67.42: 42 67.42 - 84.27: 15 Dihedral angle restraints: 2767 sinusoidal: 1150 harmonic: 1617 Sorted by residual: dihedral pdb=" CG ARG E 304 " pdb=" CD ARG E 304 " pdb=" NE ARG E 304 " pdb=" CZ ARG E 304 " ideal model delta sinusoidal sigma weight residual 180.00 136.41 43.59 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA ASP C 137 " pdb=" CB ASP C 137 " pdb=" CG ASP C 137 " pdb=" OD1 ASP C 137 " ideal model delta sinusoidal sigma weight residual -30.00 -83.50 53.50 1 2.00e+01 2.50e-03 9.72e+00 dihedral pdb=" CB GLU C 60 " pdb=" CG GLU C 60 " pdb=" CD GLU C 60 " pdb=" OE1 GLU C 60 " ideal model delta sinusoidal sigma weight residual 0.00 84.07 -84.07 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 2764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 475 0.034 - 0.068: 158 0.068 - 0.102: 47 0.102 - 0.136: 22 0.136 - 0.170: 2 Chirality restraints: 704 Sorted by residual: chirality pdb=" CG LEU E 158 " pdb=" CB LEU E 158 " pdb=" CD1 LEU E 158 " pdb=" CD2 LEU E 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CG LEU E 108 " pdb=" CB LEU E 108 " pdb=" CD1 LEU E 108 " pdb=" CD2 LEU E 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 701 not shown) Planarity restraints: 805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 302 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" CD GLN E 302 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLN E 302 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN E 302 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 146 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO E 147 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 147 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 147 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 340 " -0.100 9.50e-02 1.11e+02 4.52e-02 1.59e+00 pdb=" NE ARG E 340 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 340 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 340 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 340 " -0.000 2.00e-02 2.50e+03 ... (remaining 802 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 350 2.74 - 3.28: 4143 3.28 - 3.82: 7834 3.82 - 4.36: 9191 4.36 - 4.90: 15677 Nonbonded interactions: 37195 Sorted by model distance: nonbonded pdb=" OG1 THR E 179 " pdb=" O ASP E 183 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASP E 316 " pdb=" NE1 TRP C 105 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN C 133 " pdb=" NH2 ARG C 150 " model vdw 2.275 3.120 nonbonded pdb=" O PRO E 221 " pdb=" OG SER E 224 " model vdw 2.313 3.040 nonbonded pdb=" OE2 GLU C 109 " pdb=" NH1 ARG C 112 " model vdw 2.341 3.120 ... (remaining 37190 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 'C' and (resid 54 through 203 or resid 217 through 348)) selection = (chain 'E' and ((resid 54 and (name N or name CA or name C or name O or name CB \ )) or resid 55 or (resid 56 and (name N or name CA or name C or name O or name C \ B )) or resid 57 through 181 or resid 192 through 348)) } 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.130 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4542 Z= 0.201 Angle : 0.626 7.556 6164 Z= 0.339 Chirality : 0.041 0.170 704 Planarity : 0.005 0.045 805 Dihedral : 19.396 84.270 1711 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.46 % Allowed : 28.48 % Favored : 70.06 % 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: 0.80 (0.35), residues: 548 helix: 0.77 (0.37), residues: 211 sheet: 1.11 (0.50), residues: 105 loop : 0.19 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 81 HIS 0.003 0.001 HIS E 101 PHE 0.014 0.002 PHE E 314 TYR 0.012 0.002 TYR E 278 ARG 0.010 0.001 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.563 Fit side-chains REVERT: E 160 LYS cc_start: 0.8099 (mptt) cc_final: 0.7413 (mppt) REVERT: C 74 ARG cc_start: 0.7578 (ptm160) cc_final: 0.7356 (ptp-170) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 1.6591 time to fit residues: 102.5971 Evaluate side-chains 54 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 333 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN E 302 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4542 Z= 0.163 Angle : 0.505 5.982 6164 Z= 0.259 Chirality : 0.039 0.127 704 Planarity : 0.004 0.030 805 Dihedral : 5.299 40.248 615 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.53 % Allowed : 24.95 % Favored : 71.52 % 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: 1.07 (0.35), residues: 548 helix: 1.17 (0.38), residues: 212 sheet: 0.99 (0.50), residues: 105 loop : 0.30 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 81 HIS 0.003 0.001 HIS E 101 PHE 0.011 0.001 PHE E 314 TYR 0.012 0.002 TYR E 278 ARG 0.004 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: E 119 VAL cc_start: 0.8951 (m) cc_final: 0.8551 (t) REVERT: E 160 LYS cc_start: 0.8067 (mptt) cc_final: 0.7399 (mppt) REVERT: E 272 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: E 306 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: E 321 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8140 (tp) REVERT: C 74 ARG cc_start: 0.7801 (ptm160) cc_final: 0.7568 (ptp-170) REVERT: C 299 TYR cc_start: 0.8062 (m-80) cc_final: 0.5672 (t80) outliers start: 17 outliers final: 6 residues processed: 70 average time/residue: 1.4855 time to fit residues: 107.4703 Evaluate side-chains 64 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4542 Z= 0.244 Angle : 0.541 6.271 6164 Z= 0.275 Chirality : 0.041 0.131 704 Planarity : 0.004 0.029 805 Dihedral : 4.456 25.416 604 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.78 % Allowed : 23.91 % Favored : 71.31 % 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: 1.07 (0.35), residues: 548 helix: 1.15 (0.38), residues: 212 sheet: 0.96 (0.50), residues: 105 loop : 0.33 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 81 HIS 0.003 0.001 HIS C 163 PHE 0.014 0.002 PHE E 294 TYR 0.015 0.002 TYR E 278 ARG 0.004 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: E 74 ARG cc_start: 0.7423 (ptm160) cc_final: 0.7218 (ptm160) REVERT: E 119 VAL cc_start: 0.8969 (m) cc_final: 0.8680 (t) REVERT: E 160 LYS cc_start: 0.8075 (mptt) cc_final: 0.7415 (mppt) REVERT: E 272 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: E 306 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: E 321 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8261 (tp) outliers start: 23 outliers final: 9 residues processed: 83 average time/residue: 1.4517 time to fit residues: 124.5195 Evaluate side-chains 74 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 191 GLN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4542 Z= 0.365 Angle : 0.619 7.369 6164 Z= 0.312 Chirality : 0.043 0.134 704 Planarity : 0.005 0.031 805 Dihedral : 4.914 26.249 604 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.86 % Allowed : 21.62 % Favored : 71.52 % 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: 0.79 (0.35), residues: 548 helix: 0.91 (0.37), residues: 212 sheet: 0.52 (0.46), residues: 124 loop : 0.32 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 105 HIS 0.004 0.001 HIS C 163 PHE 0.016 0.002 PHE E 294 TYR 0.017 0.003 TYR E 278 ARG 0.005 0.001 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8110 (mttt) REVERT: E 119 VAL cc_start: 0.9020 (m) cc_final: 0.8691 (t) REVERT: E 160 LYS cc_start: 0.8073 (mptt) cc_final: 0.7403 (mppt) REVERT: E 306 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: C 133 ASN cc_start: 0.7871 (m-40) cc_final: 0.7601 (t0) REVERT: C 174 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6531 (pttp) outliers start: 33 outliers final: 15 residues processed: 90 average time/residue: 1.5320 time to fit residues: 142.1557 Evaluate side-chains 84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 GLN E 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4542 Z= 0.238 Angle : 0.541 6.135 6164 Z= 0.274 Chirality : 0.040 0.133 704 Planarity : 0.004 0.032 805 Dihedral : 4.644 25.001 604 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.16 % Allowed : 24.95 % Favored : 70.89 % 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: 0.85 (0.36), residues: 548 helix: 1.03 (0.37), residues: 218 sheet: 0.56 (0.46), residues: 122 loop : 0.25 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.003 0.001 HIS E 101 PHE 0.014 0.002 PHE E 314 TYR 0.016 0.002 TYR E 278 ARG 0.006 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: E 160 LYS cc_start: 0.8091 (mptt) cc_final: 0.7424 (mppt) REVERT: E 306 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: C 174 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6578 (pttp) outliers start: 20 outliers final: 9 residues processed: 80 average time/residue: 1.5690 time to fit residues: 129.2625 Evaluate side-chains 72 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4542 Z= 0.252 Angle : 0.544 5.715 6164 Z= 0.275 Chirality : 0.040 0.133 704 Planarity : 0.004 0.032 805 Dihedral : 4.632 25.103 604 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.78 % Allowed : 24.12 % Favored : 71.10 % 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: 0.88 (0.36), residues: 548 helix: 1.08 (0.37), residues: 218 sheet: 0.52 (0.45), residues: 124 loop : 0.28 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.003 0.001 HIS E 101 PHE 0.014 0.002 PHE E 314 TYR 0.016 0.002 TYR E 278 ARG 0.006 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: E 160 LYS cc_start: 0.8092 (mptt) cc_final: 0.7396 (mppt) REVERT: E 306 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: C 174 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6595 (pttp) outliers start: 23 outliers final: 12 residues processed: 82 average time/residue: 1.5115 time to fit residues: 127.7071 Evaluate side-chains 78 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 260 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8318 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4542 Z= 0.192 Angle : 0.510 5.139 6164 Z= 0.260 Chirality : 0.039 0.132 704 Planarity : 0.004 0.036 805 Dihedral : 4.455 23.950 604 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.37 % Allowed : 24.95 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.36), residues: 548 helix: 1.26 (0.38), residues: 218 sheet: 0.45 (0.49), residues: 109 loop : 0.26 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 105 HIS 0.003 0.001 HIS E 101 PHE 0.014 0.002 PHE E 314 TYR 0.014 0.002 TYR E 278 ARG 0.006 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: E 74 ARG cc_start: 0.7175 (ptp90) cc_final: 0.6957 (ptt180) REVERT: E 160 LYS cc_start: 0.7993 (mptt) cc_final: 0.7347 (mppt) REVERT: E 225 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8455 (mt-10) REVERT: E 306 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: C 299 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6164 (t80) outliers start: 21 outliers final: 9 residues processed: 82 average time/residue: 1.4783 time to fit residues: 125.1025 Evaluate side-chains 74 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 299 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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: 0.8283 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4542 Z= 0.148 Angle : 0.493 4.805 6164 Z= 0.250 Chirality : 0.039 0.132 704 Planarity : 0.004 0.033 805 Dihedral : 4.293 22.812 604 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.33 % Allowed : 27.03 % Favored : 69.65 % 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: 1.21 (0.36), residues: 548 helix: 1.52 (0.38), residues: 212 sheet: 0.49 (0.50), residues: 109 loop : 0.43 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 81 HIS 0.003 0.000 HIS E 101 PHE 0.013 0.001 PHE E 314 TYR 0.013 0.001 TYR E 278 ARG 0.005 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: E 225 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8433 (mt-10) REVERT: E 272 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: E 306 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: C 299 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.5973 (t80) outliers start: 16 outliers final: 8 residues processed: 78 average time/residue: 1.4930 time to fit residues: 120.2510 Evaluate side-chains 73 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 299 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 0.0470 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- 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: 0.8324 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4542 Z= 0.239 Angle : 0.555 5.828 6164 Z= 0.278 Chirality : 0.041 0.132 704 Planarity : 0.004 0.038 805 Dihedral : 4.521 24.333 604 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.53 % Allowed : 27.23 % Favored : 69.23 % 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: 1.12 (0.36), residues: 548 helix: 1.41 (0.38), residues: 212 sheet: 0.45 (0.46), residues: 122 loop : 0.42 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 81 HIS 0.002 0.001 HIS E 101 PHE 0.013 0.002 PHE E 314 TYR 0.014 0.002 TYR E 278 ARG 0.006 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: E 225 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8431 (mt-10) REVERT: E 306 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: C 174 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6847 (pttp) outliers start: 17 outliers final: 8 residues processed: 76 average time/residue: 1.5469 time to fit residues: 121.3636 Evaluate side-chains 74 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.0870 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4542 Z= 0.211 Angle : 0.544 6.335 6164 Z= 0.274 Chirality : 0.041 0.137 704 Planarity : 0.004 0.033 805 Dihedral : 4.509 23.594 604 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.70 % Allowed : 28.48 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.36), residues: 548 helix: 1.41 (0.38), residues: 212 sheet: 0.41 (0.46), residues: 122 loop : 0.42 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 81 HIS 0.002 0.001 HIS E 101 PHE 0.013 0.002 PHE E 314 TYR 0.013 0.002 TYR E 278 ARG 0.006 0.000 ARG E 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: E 225 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8451 (mt-10) REVERT: E 306 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: C 174 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6894 (pttp) REVERT: C 299 TYR cc_start: 0.8155 (m-80) cc_final: 0.6158 (t80) outliers start: 13 outliers final: 8 residues processed: 74 average time/residue: 1.5779 time to fit residues: 120.4733 Evaluate side-chains 71 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.0980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.166363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.126974 restraints weight = 4597.871| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.12 r_work: 0.3015 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4542 Z= 0.171 Angle : 0.522 5.737 6164 Z= 0.263 Chirality : 0.040 0.139 704 Planarity : 0.004 0.034 805 Dihedral : 4.371 22.720 604 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.33 % Allowed : 28.07 % Favored : 68.61 % 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: 1.18 (0.36), residues: 548 helix: 1.52 (0.38), residues: 212 sheet: 0.50 (0.50), residues: 104 loop : 0.37 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 81 HIS 0.003 0.000 HIS E 101 PHE 0.013 0.001 PHE E 314 TYR 0.013 0.002 TYR E 278 ARG 0.009 0.000 ARG E 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.11 seconds wall clock time: 43 minutes 9.36 seconds (2589.36 seconds total)