Starting phenix.real_space_refine on Fri Dec 27 13:40:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0k_24107/12_2024/7n0k_24107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0k_24107/12_2024/7n0k_24107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n0k_24107/12_2024/7n0k_24107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0k_24107/12_2024/7n0k_24107.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0k_24107/12_2024/7n0k_24107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0k_24107/12_2024/7n0k_24107.cif" } resolution = 3.5 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= 0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3404 2.51 5 N 852 2.21 5 O 868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5154 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2577 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 39 Restraints were copied for chains: B Time building chain proxies: 7.12, per 1000 atoms: 1.38 Number of scatterers: 5154 At special positions: 0 Unit cell: (97.85, 91.67, 90.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 868 8.00 N 852 7.00 C 3404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 611.1 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'B' and resid 9 through 68 removed outlier: 4.273A pdb=" N TRP B 16 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 101 removed outlier: 3.907A pdb=" N ALA B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 122 through 154 removed outlier: 3.832A pdb=" N LYS B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.698A pdb=" N ILE B 177 " --> pdb=" O CYS B 173 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 4.079A pdb=" N VAL B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.585A pdb=" N LYS B 218 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 250 removed outlier: 3.968A pdb=" N PHE B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 298 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 305 through 335 removed outlier: 3.857A pdb=" N MET B 309 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 3.585A pdb=" N PHE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 68 removed outlier: 4.273A pdb=" N TRP A 16 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 101 removed outlier: 3.906A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.832A pdb=" N LYS A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.699A pdb=" N ILE A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 removed outlier: 4.078A pdb=" N VAL A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.585A pdb=" N LYS A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 250 removed outlier: 3.967A pdb=" N PHE A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 243 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 298 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 305 through 335 removed outlier: 3.858A pdb=" N MET A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix removed outlier: 3.584A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1576 1.34 - 1.46: 1379 1.46 - 1.58: 2297 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5296 Sorted by residual: bond pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C TRP A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.20e-02 6.94e+03 7.61e-01 bond pdb=" C TRP B 210 " pdb=" N PRO B 211 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.20e-02 6.94e+03 7.52e-01 bond pdb=" N GLY A 213 " pdb=" CA GLY A 213 " ideal model delta sigma weight residual 1.455 1.447 0.008 1.05e-02 9.07e+03 5.51e-01 ... (remaining 5291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7005 1.53 - 3.07: 133 3.07 - 4.60: 18 4.60 - 6.14: 4 6.14 - 7.67: 4 Bond angle restraints: 7164 Sorted by residual: angle pdb=" CA GLN B 124 " pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLN A 124 " pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " pdb=" CD GLN A 124 " ideal model delta sigma weight residual 112.60 116.00 -3.40 1.70e+00 3.46e-01 3.99e+00 angle pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " pdb=" CD GLN B 124 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.70e+00 3.46e-01 3.93e+00 angle pdb=" CA LEU A 120 " pdb=" CB LEU A 120 " pdb=" CG LEU A 120 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.35e+00 ... (remaining 7159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2586 17.87 - 35.74: 340 35.74 - 53.62: 92 53.62 - 71.49: 14 71.49 - 89.36: 14 Dihedral angle restraints: 3046 sinusoidal: 1208 harmonic: 1838 Sorted by residual: dihedral pdb=" CA LEU B 120 " pdb=" C LEU B 120 " pdb=" N LEU B 121 " pdb=" CA LEU B 121 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LEU A 120 " pdb=" C LEU A 120 " pdb=" N LEU A 121 " pdb=" CA LEU A 121 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU A 60 " pdb=" CG GLU A 60 " pdb=" CD GLU A 60 " pdb=" OE1 GLU A 60 " ideal model delta sinusoidal sigma weight residual 0.00 -89.36 89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 498 0.025 - 0.050: 203 0.050 - 0.075: 53 0.075 - 0.100: 9 0.100 - 0.125: 9 Chirality restraints: 772 Sorted by residual: chirality pdb=" CA VAL A 112 " pdb=" N VAL A 112 " pdb=" C VAL A 112 " pdb=" CB VAL A 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 769 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 312 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 313 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 312 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 313 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 69 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 70 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.017 5.00e-02 4.00e+02 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1129 2.77 - 3.30: 5182 3.30 - 3.84: 8155 3.84 - 4.37: 9401 4.37 - 4.90: 15378 Nonbonded interactions: 39245 Sorted by model distance: nonbonded pdb=" O LYS A 137 " pdb=" OG1 THR A 141 " model vdw 2.238 3.040 nonbonded pdb=" O LYS B 137 " pdb=" OG1 THR B 141 " model vdw 2.239 3.040 nonbonded pdb=" O GLN A 44 " pdb=" OG1 THR A 48 " model vdw 2.266 3.040 nonbonded pdb=" O GLN B 44 " pdb=" OG1 THR B 48 " model vdw 2.266 3.040 nonbonded pdb=" O GLU A 38 " pdb=" OG1 THR A 41 " model vdw 2.310 3.040 ... (remaining 39240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 10.120 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 22.550 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:4.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5296 Z= 0.197 Angle : 0.558 7.672 7164 Z= 0.320 Chirality : 0.031 0.125 772 Planarity : 0.003 0.035 888 Dihedral : 18.365 89.361 1858 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 7.46 % Allowed : 17.16 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.29), residues: 614 helix: -1.29 (0.18), residues: 526 sheet: None (None), residues: 0 loop : -1.07 (0.76), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.003 0.001 HIS A 196 PHE 0.007 0.001 PHE B 127 TYR 0.007 0.001 TYR A 172 ARG 0.005 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7238 (t80) cc_final: 0.6972 (t80) REVERT: A 127 PHE cc_start: 0.7398 (t80) cc_final: 0.7135 (t80) REVERT: A 183 ILE cc_start: 0.7261 (mm) cc_final: 0.6926 (mt) REVERT: A 228 MET cc_start: 0.7126 (mtm) cc_final: 0.6891 (ttm) outliers start: 40 outliers final: 22 residues processed: 130 average time/residue: 0.2159 time to fit residues: 36.4773 Evaluate side-chains 90 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.0040 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS B 197 HIS B 241 GLN B 286 GLN A 184 ASN A 196 HIS A 197 HIS A 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5296 Z= 0.186 Angle : 0.576 8.405 7164 Z= 0.295 Chirality : 0.035 0.123 772 Planarity : 0.005 0.057 888 Dihedral : 8.243 85.589 718 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.73 % Allowed : 23.32 % Favored : 72.95 % 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: 1.25 (0.31), residues: 614 helix: 1.27 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -2.23 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 192 HIS 0.004 0.001 HIS A 30 PHE 0.013 0.001 PHE B 195 TYR 0.013 0.001 TYR B 240 ARG 0.003 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.615 Fit side-chains REVERT: B 118 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8197 (t) REVERT: B 158 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6234 (tpt-90) REVERT: B 291 LEU cc_start: 0.9006 (mm) cc_final: 0.8514 (tt) REVERT: A 87 MET cc_start: 0.7317 (tpp) cc_final: 0.6795 (tpt) REVERT: A 158 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6427 (tpt-90) outliers start: 20 outliers final: 11 residues processed: 98 average time/residue: 0.1908 time to fit residues: 24.3757 Evaluate side-chains 81 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 55 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN A 30 HIS A 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5296 Z= 0.213 Angle : 0.540 5.893 7164 Z= 0.273 Chirality : 0.035 0.120 772 Planarity : 0.004 0.048 888 Dihedral : 7.338 83.364 704 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.60 % Allowed : 25.75 % Favored : 68.66 % 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: 2.12 (0.32), residues: 614 helix: 1.84 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -1.56 (0.58), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.001 0.000 HIS A 196 PHE 0.008 0.001 PHE A 235 TYR 0.016 0.002 TYR B 240 ARG 0.007 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7395 (t80) cc_final: 0.6303 (m-10) REVERT: B 158 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6342 (tpt-90) REVERT: B 234 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6978 (mp10) REVERT: B 291 LEU cc_start: 0.9022 (mm) cc_final: 0.8774 (mp) REVERT: A 88 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8159 (mtmt) REVERT: A 127 PHE cc_start: 0.7353 (t80) cc_final: 0.6538 (m-10) REVERT: A 158 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6499 (tpt-90) REVERT: A 183 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6888 (mt) outliers start: 30 outliers final: 18 residues processed: 97 average time/residue: 0.1765 time to fit residues: 22.2929 Evaluate side-chains 90 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5296 Z= 0.152 Angle : 0.501 8.744 7164 Z= 0.248 Chirality : 0.034 0.129 772 Planarity : 0.003 0.041 888 Dihedral : 6.688 77.793 701 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.66 % Allowed : 28.92 % Favored : 66.42 % 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: 2.80 (0.32), residues: 614 helix: 2.32 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.79 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.001 0.000 HIS A 196 PHE 0.007 0.001 PHE A 94 TYR 0.014 0.001 TYR B 240 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6260 (tpt-90) REVERT: B 291 LEU cc_start: 0.8840 (mm) cc_final: 0.8347 (tt) REVERT: A 88 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8103 (mttt) REVERT: A 158 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6309 (tpt-90) outliers start: 25 outliers final: 12 residues processed: 91 average time/residue: 0.1679 time to fit residues: 20.0459 Evaluate side-chains 77 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5296 Z= 0.179 Angle : 0.528 7.702 7164 Z= 0.255 Chirality : 0.034 0.129 772 Planarity : 0.003 0.032 888 Dihedral : 4.845 51.420 691 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.41 % Allowed : 29.29 % Favored : 65.30 % 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: 3.10 (0.33), residues: 614 helix: 2.54 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.81 (0.60), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.001 0.000 HIS B 196 PHE 0.009 0.001 PHE A 195 TYR 0.015 0.001 TYR B 240 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7128 (t80) cc_final: 0.6352 (m-10) REVERT: B 158 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6314 (tpt-90) REVERT: B 208 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7643 (tp) REVERT: B 291 LEU cc_start: 0.8883 (mm) cc_final: 0.8640 (mp) REVERT: A 127 PHE cc_start: 0.7337 (t80) cc_final: 0.6580 (m-10) REVERT: A 158 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6348 (tpt-90) REVERT: A 208 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7669 (tp) outliers start: 29 outliers final: 20 residues processed: 87 average time/residue: 0.1885 time to fit residues: 21.8484 Evaluate side-chains 87 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.0070 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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: 0.7345 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5296 Z= 0.175 Angle : 0.527 8.923 7164 Z= 0.252 Chirality : 0.034 0.129 772 Planarity : 0.003 0.028 888 Dihedral : 4.653 46.722 691 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.41 % Allowed : 30.22 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.33 (0.33), residues: 614 helix: 2.69 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.75 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 210 HIS 0.001 0.000 HIS B 196 PHE 0.008 0.001 PHE A 195 TYR 0.019 0.001 TYR B 240 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6269 (tpt-90) REVERT: B 208 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7635 (tp) REVERT: B 291 LEU cc_start: 0.8895 (mm) cc_final: 0.8656 (mp) REVERT: A 127 PHE cc_start: 0.7266 (t80) cc_final: 0.6572 (m-10) REVERT: A 158 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6283 (tpt-90) REVERT: A 208 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7755 (tp) REVERT: A 304 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5935 (mm-30) outliers start: 29 outliers final: 18 residues processed: 85 average time/residue: 0.1667 time to fit residues: 18.9066 Evaluate side-chains 85 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 37 optimal weight: 0.0770 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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: 0.7298 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5296 Z= 0.150 Angle : 0.519 8.848 7164 Z= 0.248 Chirality : 0.033 0.132 772 Planarity : 0.003 0.028 888 Dihedral : 4.507 42.794 691 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.04 % Allowed : 32.09 % Favored : 62.87 % 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: 3.55 (0.33), residues: 614 helix: 2.85 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.74 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.001 0.000 HIS A 30 PHE 0.009 0.001 PHE B 195 TYR 0.012 0.001 TYR B 240 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6253 (tpt-90) REVERT: B 208 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7654 (tp) REVERT: B 291 LEU cc_start: 0.8866 (mm) cc_final: 0.8446 (tt) REVERT: A 158 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6261 (tpt-90) REVERT: A 208 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7837 (tp) outliers start: 27 outliers final: 15 residues processed: 85 average time/residue: 0.1892 time to fit residues: 20.8921 Evaluate side-chains 79 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 291 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5296 Z= 0.192 Angle : 0.552 9.247 7164 Z= 0.264 Chirality : 0.034 0.132 772 Planarity : 0.003 0.029 888 Dihedral : 3.871 18.162 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.78 % Allowed : 31.34 % Favored : 62.87 % 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: 3.46 (0.33), residues: 614 helix: 2.79 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.79 (0.62), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 196 PHE 0.010 0.001 PHE B 195 TYR 0.023 0.002 TYR B 240 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6242 (tpt-90) REVERT: B 208 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7724 (tp) REVERT: B 291 LEU cc_start: 0.8854 (mm) cc_final: 0.8608 (mp) REVERT: A 81 GLN cc_start: 0.6668 (mp10) cc_final: 0.6438 (mp10) REVERT: A 84 GLU cc_start: 0.6562 (tm-30) cc_final: 0.6249 (tm-30) REVERT: A 91 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: A 127 PHE cc_start: 0.7290 (t80) cc_final: 0.6540 (m-10) REVERT: A 158 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6172 (tpt-90) outliers start: 31 outliers final: 20 residues processed: 91 average time/residue: 0.1550 time to fit residues: 18.6823 Evaluate side-chains 91 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7361 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5296 Z= 0.204 Angle : 0.564 9.863 7164 Z= 0.270 Chirality : 0.034 0.131 772 Planarity : 0.003 0.030 888 Dihedral : 3.881 17.528 686 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.78 % Allowed : 31.53 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.40 (0.33), residues: 614 helix: 2.76 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.90 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.001 0.000 HIS B 196 PHE 0.009 0.001 PHE B 195 TYR 0.024 0.002 TYR A 240 ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: B 158 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6323 (tpt-90) REVERT: B 208 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7817 (tp) REVERT: B 234 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: B 268 MET cc_start: 0.8371 (mmm) cc_final: 0.8149 (tpp) REVERT: B 291 LEU cc_start: 0.8866 (mm) cc_final: 0.8616 (mp) REVERT: A 84 GLU cc_start: 0.6557 (tm-30) cc_final: 0.6236 (tm-30) REVERT: A 127 PHE cc_start: 0.7234 (t80) cc_final: 0.6440 (m-10) outliers start: 31 outliers final: 21 residues processed: 90 average time/residue: 0.1408 time to fit residues: 17.3941 Evaluate side-chains 93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7368 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5296 Z= 0.219 Angle : 0.602 9.551 7164 Z= 0.286 Chirality : 0.034 0.129 772 Planarity : 0.003 0.030 888 Dihedral : 3.914 17.270 686 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.85 % Allowed : 32.84 % Favored : 62.31 % 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: 3.40 (0.33), residues: 614 helix: 2.73 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.65 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.001 0.000 HIS A 196 PHE 0.009 0.001 PHE B 195 TYR 0.023 0.002 TYR B 240 ARG 0.008 0.000 ARG A 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7263 (t80) cc_final: 0.6406 (m-10) REVERT: B 158 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6412 (tpt-90) REVERT: B 208 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 234 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: B 268 MET cc_start: 0.8393 (mmm) cc_final: 0.8135 (tpp) REVERT: B 291 LEU cc_start: 0.8865 (mm) cc_final: 0.8385 (tt) REVERT: A 84 GLU cc_start: 0.6563 (tm-30) cc_final: 0.6235 (tm-30) REVERT: A 127 PHE cc_start: 0.7263 (t80) cc_final: 0.6451 (m-10) outliers start: 26 outliers final: 21 residues processed: 92 average time/residue: 0.1389 time to fit residues: 17.4922 Evaluate side-chains 94 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.206090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165139 restraints weight = 5742.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.168536 restraints weight = 3562.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.170788 restraints weight = 2684.122| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5296 Z= 0.192 Angle : 0.583 9.702 7164 Z= 0.277 Chirality : 0.034 0.129 772 Planarity : 0.003 0.030 888 Dihedral : 3.872 17.576 686 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.85 % Allowed : 33.21 % Favored : 61.94 % 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: 3.53 (0.33), residues: 614 helix: 2.81 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.51 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 210 HIS 0.001 0.000 HIS A 196 PHE 0.009 0.001 PHE B 195 TYR 0.023 0.001 TYR A 240 ARG 0.009 0.001 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.26 seconds wall clock time: 25 minutes 10.75 seconds (1510.75 seconds total)