Starting phenix.real_space_refine on Tue Feb 11 09:45:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0k_24107/02_2025/7n0k_24107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0k_24107/02_2025/7n0k_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_24107/02_2025/7n0k_24107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0k_24107/02_2025/7n0k_24107.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0k_24107/02_2025/7n0k_24107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0k_24107/02_2025/7n0k_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-5592/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: 4.25, per 1000 atoms: 0.82 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: 1.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.57 Time building geometry restraints manager: 1.61 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: 0.03 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- 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 : 0.593 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: 0.1990 time to fit residues: 33.2327 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 : 0.592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.205043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164790 restraints weight = 5678.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168432 restraints weight = 3426.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170632 restraints weight = 2540.165| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 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 : 0.591 Fit side-chains REVERT: B 118 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8203 (t) REVERT: B 158 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6065 (tpt-90) REVERT: B 291 LEU cc_start: 0.8976 (mm) cc_final: 0.8367 (tt) REVERT: A 87 MET cc_start: 0.7523 (tpp) cc_final: 0.6880 (tpt) REVERT: A 158 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.6260 (tpt-90) outliers start: 20 outliers final: 11 residues processed: 98 average time/residue: 0.1764 time to fit residues: 22.6204 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 : 0.565 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS A 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.201378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.160402 restraints weight = 5810.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163929 restraints weight = 3581.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166240 restraints weight = 2676.750| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5296 Z= 0.259 Angle : 0.575 6.188 7164 Z= 0.290 Chirality : 0.037 0.120 772 Planarity : 0.004 0.050 888 Dihedral : 7.473 85.745 704 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.78 % Allowed : 26.49 % Favored : 67.72 % 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: 1.96 (0.32), residues: 614 helix: 1.74 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -2.05 (0.60), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 210 HIS 0.001 0.001 HIS A 330 PHE 0.009 0.001 PHE A 235 TYR 0.016 0.002 TYR B 240 ARG 0.006 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 106 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7502 (t80) cc_final: 0.6133 (m-10) REVERT: B 158 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6218 (tpt-90) REVERT: B 234 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: A 88 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8175 (mtmt) REVERT: A 127 PHE cc_start: 0.7369 (t80) cc_final: 0.6182 (m-10) REVERT: A 158 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6344 (tpt-90) REVERT: A 183 ILE cc_start: 0.7311 (OUTLIER) cc_final: 0.7086 (mt) outliers start: 31 outliers final: 19 residues processed: 99 average time/residue: 0.1776 time to fit residues: 22.8690 Evaluate side-chains 93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 207 MET 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 304 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.204800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164267 restraints weight = 5879.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.167701 restraints weight = 3652.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169898 restraints weight = 2756.747| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3780 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= 0.191 Angle : 0.541 10.740 7164 Z= 0.265 Chirality : 0.036 0.219 772 Planarity : 0.004 0.038 888 Dihedral : 6.883 82.928 701 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.97 % Allowed : 28.36 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.33), residues: 614 helix: 2.14 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.83 (0.62), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.001 0.000 HIS A 196 PHE 0.007 0.001 PHE A 235 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 104 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8038 (mtmt) REVERT: B 127 PHE cc_start: 0.7330 (t80) cc_final: 0.6149 (m-10) REVERT: B 158 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6121 (tpt-90) REVERT: B 208 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7433 (tp) REVERT: B 234 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.6550 (mp10) REVERT: A 88 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8098 (mttt) REVERT: A 127 PHE cc_start: 0.7344 (t80) cc_final: 0.6235 (m-10) REVERT: A 158 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6203 (tpt-90) REVERT: A 208 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7472 (tp) outliers start: 32 outliers final: 16 residues processed: 99 average time/residue: 0.1586 time to fit residues: 20.6115 Evaluate side-chains 91 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 GLN 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 183 ILE 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 304 GLU Chi-restraints excluded: chain A residue 41 THR 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 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 304 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.206495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166174 restraints weight = 5725.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.169613 restraints weight = 3603.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171781 restraints weight = 2724.554| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5296 Z= 0.171 Angle : 0.521 7.654 7164 Z= 0.255 Chirality : 0.035 0.212 772 Planarity : 0.003 0.029 888 Dihedral : 6.400 81.575 697 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.60 % Allowed : 29.66 % Favored : 64.74 % 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: 2.94 (0.33), residues: 614 helix: 2.43 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.82 (0.62), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 210 HIS 0.001 0.000 HIS B 196 PHE 0.007 0.001 PHE A 235 TYR 0.017 0.001 TYR B 240 ARG 0.003 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 101 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 MET cc_start: 0.7732 (mmt) cc_final: 0.7468 (tpt) REVERT: B 158 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.6084 (tpt-90) REVERT: B 208 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7349 (tp) REVERT: B 234 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: A 88 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7979 (mtmt) REVERT: A 127 PHE cc_start: 0.7342 (t80) cc_final: 0.6234 (m-10) REVERT: A 158 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6108 (tpt-90) REVERT: A 228 MET cc_start: 0.7504 (mmm) cc_final: 0.7203 (mmm) outliers start: 30 outliers final: 21 residues processed: 95 average time/residue: 0.1646 time to fit residues: 20.6482 Evaluate side-chains 87 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 120 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 183 ILE 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 291 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.205561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164410 restraints weight = 5798.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168003 restraints weight = 3553.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170069 restraints weight = 2647.453| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5296 Z= 0.186 Angle : 0.530 8.505 7164 Z= 0.258 Chirality : 0.035 0.215 772 Planarity : 0.003 0.029 888 Dihedral : 6.264 81.830 697 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 6.90 % Allowed : 29.48 % Favored : 63.62 % 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: 3.08 (0.33), residues: 614 helix: 2.53 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.82 (0.63), 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 0.010 0.001 PHE B 195 TYR 0.022 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 106 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7923 (mtmt) REVERT: B 158 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6111 (tpt-90) REVERT: B 208 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7339 (tp) REVERT: B 230 GLN cc_start: 0.7300 (tt0) cc_final: 0.6864 (tt0) REVERT: B 234 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: B 304 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6009 (mm-30) REVERT: B 309 MET cc_start: 0.7627 (tpp) cc_final: 0.7401 (tpp) REVERT: A 88 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8087 (mttt) REVERT: A 127 PHE cc_start: 0.7240 (t80) cc_final: 0.6109 (m-10) REVERT: A 158 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6092 (tpt-90) REVERT: A 309 MET cc_start: 0.7620 (tpp) cc_final: 0.7406 (tpp) outliers start: 37 outliers final: 27 residues processed: 99 average time/residue: 0.1627 time to fit residues: 21.1832 Evaluate side-chains 99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 91 GLN 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 183 ILE 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 304 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 113 LEU 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 328 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.203289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.160649 restraints weight = 5812.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.164680 restraints weight = 3358.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167177 restraints weight = 2428.825| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4261 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= 0.212 Angle : 0.546 6.943 7164 Z= 0.265 Chirality : 0.035 0.228 772 Planarity : 0.003 0.029 888 Dihedral : 5.942 84.456 694 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 6.72 % Allowed : 29.29 % Favored : 63.99 % 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: 2.55 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.90 (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 0.009 0.001 PHE B 195 TYR 0.018 0.002 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 105 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7871 (mtmt) REVERT: B 89 GLU cc_start: 0.7593 (tt0) cc_final: 0.7387 (pt0) REVERT: B 127 PHE cc_start: 0.7276 (t80) cc_final: 0.6167 (m-10) REVERT: B 158 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6377 (tpt-90) REVERT: B 208 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7537 (tp) REVERT: B 234 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6425 (mp10) REVERT: B 304 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6214 (mm-30) REVERT: A 88 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8034 (mttt) REVERT: A 127 PHE cc_start: 0.7297 (t80) cc_final: 0.6189 (m-10) REVERT: A 158 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6223 (tpt-90) outliers start: 36 outliers final: 24 residues processed: 97 average time/residue: 0.1644 time to fit residues: 20.8905 Evaluate side-chains 97 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 CYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 ILE 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 304 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 113 LEU 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 183 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.205211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164000 restraints weight = 5791.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.167526 restraints weight = 3574.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.169826 restraints weight = 2683.414| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4400 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= 0.187 Angle : 0.566 11.014 7164 Z= 0.267 Chirality : 0.035 0.239 772 Planarity : 0.003 0.029 888 Dihedral : 5.819 83.034 694 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.97 % Allowed : 31.53 % Favored : 62.50 % 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: 3.23 (0.33), residues: 614 helix: 2.65 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.99 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.001 0.000 HIS B 196 PHE 0.009 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 98 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7873 (mtmt) REVERT: B 89 GLU cc_start: 0.7776 (tt0) cc_final: 0.7497 (pt0) REVERT: B 158 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6306 (tpt-90) REVERT: B 208 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7410 (tp) REVERT: B 234 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6403 (mp10) REVERT: B 309 MET cc_start: 0.7628 (tpp) cc_final: 0.7361 (tpp) REVERT: A 88 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8010 (mttt) REVERT: A 127 PHE cc_start: 0.7234 (t80) cc_final: 0.6123 (m-10) REVERT: A 158 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6111 (tpt-90) REVERT: A 309 MET cc_start: 0.7611 (tpp) cc_final: 0.7332 (tpp) outliers start: 32 outliers final: 25 residues processed: 89 average time/residue: 0.1670 time to fit residues: 19.5183 Evaluate side-chains 95 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 151 CYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 ILE 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 291 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 113 LEU 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 183 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 0.0070 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.208049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166993 restraints weight = 5771.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170643 restraints weight = 3556.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173043 restraints weight = 2646.998| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5296 Z= 0.151 Angle : 0.544 9.718 7164 Z= 0.255 Chirality : 0.034 0.249 772 Planarity : 0.003 0.030 888 Dihedral : 5.403 80.174 691 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.04 % Allowed : 32.84 % Favored : 62.13 % 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: 3.42 (0.33), residues: 614 helix: 2.78 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.97 (0.60), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.001 0.000 HIS A 30 PHE 0.009 0.001 PHE B 195 TYR 0.018 0.001 TYR A 240 ARG 0.002 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 95 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7860 (mtmt) REVERT: B 158 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6217 (tpt-90) REVERT: B 230 GLN cc_start: 0.7384 (tt0) cc_final: 0.6989 (tt0) REVERT: B 234 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6477 (mp10) REVERT: B 240 TYR cc_start: 0.7418 (t80) cc_final: 0.6882 (t80) REVERT: B 309 MET cc_start: 0.7686 (tpp) cc_final: 0.7435 (tpp) REVERT: A 88 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8037 (mttt) REVERT: A 158 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6027 (tpt-90) REVERT: A 240 TYR cc_start: 0.7299 (t80) cc_final: 0.6770 (t80) REVERT: A 309 MET cc_start: 0.7652 (tpp) cc_final: 0.7415 (tpp) outliers start: 27 outliers final: 19 residues processed: 86 average time/residue: 0.1711 time to fit residues: 19.3387 Evaluate side-chains 87 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 151 CYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 ILE 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 328 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 120 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 183 ILE Chi-restraints excluded: chain A residue 208 LEU 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 52 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.203413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161001 restraints weight = 5872.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.164951 restraints weight = 3387.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167451 restraints weight = 2452.287| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4592 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= 0.217 Angle : 0.582 9.445 7164 Z= 0.273 Chirality : 0.035 0.132 772 Planarity : 0.003 0.029 888 Dihedral : 5.352 83.858 689 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.41 % Allowed : 32.09 % Favored : 62.50 % 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: 3.26 (0.33), residues: 614 helix: 2.68 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -2.11 (0.59), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 210 HIS 0.002 0.001 HIS A 196 PHE 0.009 0.001 PHE B 195 TYR 0.016 0.002 TYR A 240 ARG 0.003 0.000 ARG A 34 ********************** 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 97 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8349 (mtmt) cc_final: 0.7951 (mtmt) REVERT: B 127 PHE cc_start: 0.7174 (t80) cc_final: 0.6054 (m-10) REVERT: B 158 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6160 (tpt-90) REVERT: B 234 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6238 (mp10) REVERT: B 309 MET cc_start: 0.7693 (tpp) cc_final: 0.7399 (tpp) REVERT: A 88 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8005 (mttt) REVERT: A 127 PHE cc_start: 0.7185 (t80) cc_final: 0.6083 (m-10) REVERT: A 158 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.6100 (tpt-90) REVERT: A 309 MET cc_start: 0.7678 (tpp) cc_final: 0.7425 (tpp) outliers start: 29 outliers final: 23 residues processed: 89 average time/residue: 0.1905 time to fit residues: 22.0537 Evaluate side-chains 92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 151 CYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 ILE 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 328 VAL Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 113 LEU 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 183 ILE 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 14 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.203165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.161213 restraints weight = 5870.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.164978 restraints weight = 3417.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.167374 restraints weight = 2490.331| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4621 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= 0.212 Angle : 0.590 9.072 7164 Z= 0.276 Chirality : 0.035 0.133 772 Planarity : 0.003 0.029 888 Dihedral : 5.383 84.286 689 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.22 % Allowed : 32.46 % 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: 3.26 (0.33), residues: 614 helix: 2.67 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.98 (0.63), 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 0.008 0.001 PHE B 195 TYR 0.023 0.002 TYR A 240 ARG 0.009 0.000 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.48 seconds wall clock time: 32 minutes 41.56 seconds (1961.56 seconds total)