Starting phenix.real_space_refine on Thu Mar 6 04:30:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kue_23036/03_2025/7kue_23036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kue_23036/03_2025/7kue_23036.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/7kue_23036/03_2025/7kue_23036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kue_23036/03_2025/7kue_23036.map" model { file = "/net/cci-nas-00/data/ceres_data/7kue_23036/03_2025/7kue_23036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kue_23036/03_2025/7kue_23036.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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 S 24 5.16 5 C 3049 2.51 5 N 780 2.21 5 O 866 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4726 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 499 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2342 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1854 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.58, per 1000 atoms: 0.76 Number of scatterers: 4726 At special positions: 0 Unit cell: (76.36, 83.83, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 24 16.00 P 3 15.00 Al 1 13.00 F 3 9.00 O 866 8.00 N 780 7.00 C 3049 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: 1.15 Conformation dependent library (CDL) restraints added in 595.9 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 49.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'C' and resid 284 through 287 removed outlier: 3.523A pdb=" N HIS C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.093A pdb=" N ILE C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.787A pdb=" N ALA C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 removed outlier: 3.988A pdb=" N ILE A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 3.775A pdb=" N VAL A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 123 removed outlier: 3.547A pdb=" N ALA A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TRP A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.771A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 185 through 201 removed outlier: 3.916A pdb=" N TRP A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 4.105A pdb=" N GLU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.507A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 252' Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.731A pdb=" N PHE A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.772A pdb=" N MET B 57 " --> pdb=" O SER B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 111 through 131 removed outlier: 4.147A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 152 removed outlier: 4.109A pdb=" N GLU B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 174 removed outlier: 3.972A pdb=" N ILE B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N HIS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 223 through 229 removed outlier: 3.594A pdb=" N VAL B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 271 Processing helix chain 'B' and resid 272 through 275 removed outlier: 3.619A pdb=" N ASP B 275 " --> pdb=" O LEU B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.932A pdb=" N THR B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 4.070A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.883A pdb=" N VAL A 20 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 79 " --> pdb=" O ILE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 136 148 hydrogen bonds defined for protein. 432 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: 1.07 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 764 1.31 - 1.44: 1302 1.44 - 1.56: 2719 1.56 - 1.69: 10 1.69 - 1.81: 43 Bond restraints: 4838 Sorted by residual: bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 1.426 1.628 -0.202 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" N ASN B 175 " pdb=" CA ASN B 175 " ideal model delta sigma weight residual 1.462 1.373 0.089 1.46e-02 4.69e+03 3.70e+01 bond pdb=" C5 ADP A 401 " pdb=" C6 ADP A 401 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 4833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.04: 6504 7.04 - 14.07: 39 14.07 - 21.11: 4 21.11 - 28.15: 3 28.15 - 35.18: 3 Bond angle restraints: 6553 Sorted by residual: angle pdb=" N ASP A 228 " pdb=" CA ASP A 228 " pdb=" C ASP A 228 " ideal model delta sigma weight residual 112.04 143.10 -31.06 1.44e+00 4.82e-01 4.65e+02 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 111.92 128.85 -16.93 1.34e+00 5.57e-01 1.60e+02 angle pdb=" C ASP A 228 " pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " ideal model delta sigma weight residual 110.56 88.28 22.28 1.83e+00 2.99e-01 1.48e+02 angle pdb=" O2P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 113.68 78.50 35.18 3.00e+00 1.11e-01 1.38e+02 angle pdb=" O1P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 115.11 80.11 35.00 3.00e+00 1.11e-01 1.36e+02 ... (remaining 6548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 2830 32.62 - 65.24: 77 65.24 - 97.86: 4 97.86 - 130.47: 0 130.47 - 163.09: 1 Dihedral angle restraints: 2912 sinusoidal: 1200 harmonic: 1712 Sorted by residual: dihedral pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual 122.80 167.36 -44.56 0 2.50e+00 1.60e-01 3.18e+02 dihedral pdb=" C PHE B 177 " pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual -122.60 -166.19 43.59 0 2.50e+00 1.60e-01 3.04e+02 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.91 163.09 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 2909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 724 0.402 - 0.805: 4 0.805 - 1.207: 0 1.207 - 1.609: 0 1.609 - 2.012: 1 Chirality restraints: 729 Sorted by residual: chirality pdb=" CA PHE B 177 " pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CB PHE B 177 " both_signs ideal model delta sigma weight residual False 2.51 0.50 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA ASP A 228 " pdb=" N ASP A 228 " pdb=" C ASP A 228 " pdb=" CB ASP A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.67e+00 ... (remaining 726 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " -0.039 2.00e-02 2.50e+03 4.07e-02 4.15e+01 pdb=" CG TRP B 58 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 58 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 58 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 58 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 58 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 223 " -0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C THR A 223 " 0.069 2.00e-02 2.50e+03 pdb=" O THR A 223 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A 224 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 102 " 0.063 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO A 103 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.053 5.00e-02 4.00e+02 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 417 2.74 - 3.28: 4349 3.28 - 3.82: 7737 3.82 - 4.36: 8930 4.36 - 4.90: 15068 Nonbonded interactions: 36501 Sorted by model distance: nonbonded pdb=" CG PRO A 224 " pdb=" SD MET A 273 " model vdw 2.205 3.800 nonbonded pdb=" O SER A 287 " pdb=" OG SER A 287 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR A 88 " pdb=" O LEU A 135 " model vdw 2.342 3.040 nonbonded pdb=" OG SER B 153 " pdb=" OE1 GLN B 156 " model vdw 2.358 3.040 nonbonded pdb=" OD2 ASP B 224 " pdb=" OH TYR B 282 " model vdw 2.358 3.040 ... (remaining 36496 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.77 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: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 24.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 : 0.010 0.222 4838 Z= 0.585 Angle : 1.620 35.182 6553 Z= 0.815 Chirality : 0.110 2.012 729 Planarity : 0.010 0.095 821 Dihedral : 15.459 163.093 1798 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.78 % Allowed : 1.36 % Favored : 97.87 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.28), residues: 560 helix: -3.26 (0.22), residues: 258 sheet: -3.17 (0.78), residues: 35 loop : -2.66 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.006 TRP B 58 HIS 0.008 0.001 HIS A 121 PHE 0.027 0.003 PHE B 177 TYR 0.055 0.003 TYR A 57 ARG 0.013 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8250 (mm) cc_final: 0.8025 (mm) REVERT: A 49 MET cc_start: 0.7567 (tpt) cc_final: 0.7328 (tpt) REVERT: A 62 GLN cc_start: 0.6934 (mp10) cc_final: 0.6594 (mp10) REVERT: A 91 GLU cc_start: 0.7155 (pp20) cc_final: 0.6933 (pp20) REVERT: A 131 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6998 (mtmt) REVERT: A 154 ILE cc_start: 0.7867 (mt) cc_final: 0.7608 (mt) REVERT: A 184 SER cc_start: 0.8464 (t) cc_final: 0.8216 (t) REVERT: A 272 THR cc_start: 0.8194 (p) cc_final: 0.7827 (p) REVERT: B 50 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7515 (mpp-170) REVERT: B 186 LYS cc_start: 0.7224 (ttmm) cc_final: 0.6990 (ttmm) REVERT: B 246 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7946 (ttmm) REVERT: B 270 THR cc_start: 0.7898 (p) cc_final: 0.7683 (p) outliers start: 4 outliers final: 3 residues processed: 145 average time/residue: 0.1955 time to fit residues: 34.5511 Evaluate side-chains 137 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 179 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 132 ASN B 152 ASN B 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.151898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136063 restraints weight = 7698.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140141 restraints weight = 3933.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142880 restraints weight = 2373.730| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4838 Z= 0.214 Angle : 0.733 11.130 6553 Z= 0.372 Chirality : 0.048 0.217 729 Planarity : 0.008 0.073 821 Dihedral : 9.612 161.271 643 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.74 % Allowed : 10.85 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.29 (0.32), residues: 560 helix: -1.77 (0.29), residues: 266 sheet: -2.96 (0.81), residues: 34 loop : -2.46 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.015 0.002 PHE B 148 TYR 0.018 0.002 TYR B 237 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7570 (tpt) cc_final: 0.7307 (tpt) REVERT: A 57 TYR cc_start: 0.7781 (m-80) cc_final: 0.7231 (m-80) REVERT: A 62 GLN cc_start: 0.7216 (mp10) cc_final: 0.6908 (mp10) REVERT: A 91 GLU cc_start: 0.7256 (pp20) cc_final: 0.6961 (pp20) REVERT: A 154 ILE cc_start: 0.8315 (mt) cc_final: 0.8080 (mt) REVERT: A 236 MET cc_start: 0.5811 (tmm) cc_final: 0.5279 (tmm) REVERT: A 272 THR cc_start: 0.8361 (p) cc_final: 0.8016 (p) REVERT: B 50 ARG cc_start: 0.7854 (mtt90) cc_final: 0.7498 (mpp-170) REVERT: B 186 LYS cc_start: 0.7395 (ttmm) cc_final: 0.7137 (ttmm) REVERT: B 188 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7783 (mmpt) REVERT: B 246 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7987 (ttmm) outliers start: 9 outliers final: 4 residues processed: 146 average time/residue: 0.2060 time to fit residues: 36.2700 Evaluate side-chains 138 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.147873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131917 restraints weight = 7684.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136132 restraints weight = 3778.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138880 restraints weight = 2238.560| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4838 Z= 0.252 Angle : 0.704 7.421 6553 Z= 0.362 Chirality : 0.050 0.233 729 Planarity : 0.007 0.076 821 Dihedral : 8.888 147.560 640 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.33 % Allowed : 16.67 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.70 (0.33), residues: 560 helix: -1.21 (0.30), residues: 273 sheet: -2.70 (1.33), residues: 12 loop : -2.36 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 58 HIS 0.009 0.001 HIS A 121 PHE 0.013 0.002 PHE B 148 TYR 0.014 0.001 TYR B 60 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8095 (pptt) cc_final: 0.7653 (pptt) REVERT: A 38 ILE cc_start: 0.8065 (mm) cc_final: 0.7808 (mm) REVERT: A 49 MET cc_start: 0.7470 (tpt) cc_final: 0.7175 (tpt) REVERT: A 57 TYR cc_start: 0.7833 (m-80) cc_final: 0.7441 (m-80) REVERT: A 62 GLN cc_start: 0.7291 (mp10) cc_final: 0.7048 (mp10) REVERT: A 91 GLU cc_start: 0.7368 (pp20) cc_final: 0.6986 (pp20) REVERT: A 106 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 154 ILE cc_start: 0.8379 (mt) cc_final: 0.8133 (mt) REVERT: A 233 SER cc_start: 0.7898 (p) cc_final: 0.7470 (m) REVERT: A 236 MET cc_start: 0.5814 (tmm) cc_final: 0.5262 (tmm) REVERT: A 272 THR cc_start: 0.8503 (p) cc_final: 0.8081 (p) REVERT: B 50 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7574 (mpp-170) REVERT: B 246 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8019 (ttmm) outliers start: 12 outliers final: 8 residues processed: 158 average time/residue: 0.2312 time to fit residues: 44.3358 Evaluate side-chains 152 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133637 restraints weight = 7687.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137820 restraints weight = 3804.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140564 restraints weight = 2267.547| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4838 Z= 0.192 Angle : 0.666 7.021 6553 Z= 0.337 Chirality : 0.047 0.182 729 Planarity : 0.006 0.076 821 Dihedral : 8.379 135.442 640 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.29 % Allowed : 19.19 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.56 (0.34), residues: 560 helix: -1.05 (0.30), residues: 274 sheet: -2.76 (1.29), residues: 12 loop : -2.34 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 58 HIS 0.007 0.001 HIS A 127 PHE 0.020 0.001 PHE A 266 TYR 0.015 0.001 TYR B 60 ARG 0.006 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8072 (pptt) cc_final: 0.7645 (pptt) REVERT: A 49 MET cc_start: 0.7467 (tpt) cc_final: 0.7152 (tpt) REVERT: A 57 TYR cc_start: 0.7849 (m-80) cc_final: 0.7435 (m-80) REVERT: A 62 GLN cc_start: 0.7290 (mp10) cc_final: 0.7021 (mp10) REVERT: A 91 GLU cc_start: 0.7369 (pp20) cc_final: 0.6981 (pp20) REVERT: A 106 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7956 (tp) REVERT: A 128 ARG cc_start: 0.8057 (mtm180) cc_final: 0.7420 (mtm180) REVERT: A 154 ILE cc_start: 0.8411 (mt) cc_final: 0.8136 (mt) REVERT: A 233 SER cc_start: 0.7901 (p) cc_final: 0.7390 (m) REVERT: A 236 MET cc_start: 0.5755 (tmm) cc_final: 0.5225 (tmm) REVERT: A 272 THR cc_start: 0.8500 (p) cc_final: 0.8075 (p) REVERT: B 50 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7564 (mpp-170) REVERT: B 209 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7839 (tt) REVERT: B 246 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8025 (ttmm) outliers start: 17 outliers final: 12 residues processed: 154 average time/residue: 0.2442 time to fit residues: 45.7697 Evaluate side-chains 159 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.148566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132444 restraints weight = 7781.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136525 restraints weight = 3843.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139155 restraints weight = 2300.446| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4838 Z= 0.212 Angle : 0.668 6.656 6553 Z= 0.339 Chirality : 0.048 0.196 729 Planarity : 0.006 0.077 821 Dihedral : 7.937 118.941 640 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.68 % Allowed : 19.77 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.31 (0.35), residues: 560 helix: -0.83 (0.31), residues: 274 sheet: -2.65 (1.31), residues: 12 loop : -2.23 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 58 HIS 0.007 0.001 HIS A 121 PHE 0.023 0.001 PHE A 266 TYR 0.017 0.001 TYR B 60 ARG 0.006 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8088 (pptt) cc_final: 0.7640 (pptt) REVERT: A 49 MET cc_start: 0.7467 (tpt) cc_final: 0.7159 (tpt) REVERT: A 57 TYR cc_start: 0.7863 (m-80) cc_final: 0.7567 (m-80) REVERT: A 62 GLN cc_start: 0.7337 (mp10) cc_final: 0.7052 (mp10) REVERT: A 91 GLU cc_start: 0.7441 (pp20) cc_final: 0.7033 (pp20) REVERT: A 106 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7938 (tp) REVERT: A 128 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7569 (mtm180) REVERT: A 154 ILE cc_start: 0.8415 (mt) cc_final: 0.8140 (mt) REVERT: A 233 SER cc_start: 0.8001 (p) cc_final: 0.7507 (m) REVERT: A 236 MET cc_start: 0.5822 (tmm) cc_final: 0.5292 (tmm) REVERT: A 272 THR cc_start: 0.8543 (p) cc_final: 0.8120 (p) REVERT: B 50 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7571 (mpp-170) REVERT: B 209 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 222 PHE cc_start: 0.7076 (t80) cc_final: 0.6865 (t80) REVERT: B 246 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8005 (ttmm) outliers start: 19 outliers final: 13 residues processed: 153 average time/residue: 0.3208 time to fit residues: 59.5861 Evaluate side-chains 157 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.147182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.131127 restraints weight = 7737.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135225 restraints weight = 3850.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137922 restraints weight = 2291.487| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4838 Z= 0.218 Angle : 0.683 6.490 6553 Z= 0.345 Chirality : 0.048 0.180 729 Planarity : 0.006 0.078 821 Dihedral : 7.660 106.112 640 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.46 % Allowed : 21.32 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.23 (0.35), residues: 560 helix: -0.68 (0.31), residues: 273 sheet: -2.66 (1.28), residues: 12 loop : -2.30 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 58 HIS 0.006 0.001 HIS A 121 PHE 0.033 0.001 PHE A 266 TYR 0.026 0.001 TYR B 237 ARG 0.003 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8108 (pptt) cc_final: 0.7699 (pptt) REVERT: A 37 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6923 (mm-30) REVERT: A 49 MET cc_start: 0.7422 (tpt) cc_final: 0.7118 (tpt) REVERT: A 57 TYR cc_start: 0.7759 (m-80) cc_final: 0.7376 (m-80) REVERT: A 62 GLN cc_start: 0.7362 (mp10) cc_final: 0.7081 (mp10) REVERT: A 106 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7941 (tp) REVERT: A 128 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7485 (mtm180) REVERT: A 150 LEU cc_start: 0.8341 (mp) cc_final: 0.7878 (mt) REVERT: A 154 ILE cc_start: 0.8424 (mt) cc_final: 0.8167 (mt) REVERT: A 233 SER cc_start: 0.8119 (p) cc_final: 0.7646 (m) REVERT: A 236 MET cc_start: 0.5822 (tmm) cc_final: 0.5298 (tmm) REVERT: B 50 ARG cc_start: 0.7925 (mtt90) cc_final: 0.7469 (mpp-170) REVERT: B 209 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7826 (tt) REVERT: B 246 LYS cc_start: 0.8372 (ttmm) cc_final: 0.8018 (ttmm) outliers start: 23 outliers final: 15 residues processed: 151 average time/residue: 0.3537 time to fit residues: 65.0118 Evaluate side-chains 158 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 58 TRP Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 35 optimal weight: 0.3980 chunk 21 optimal weight: 0.0030 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130707 restraints weight = 7792.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134797 restraints weight = 3908.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137379 restraints weight = 2345.890| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4838 Z= 0.203 Angle : 0.676 7.047 6553 Z= 0.339 Chirality : 0.048 0.177 729 Planarity : 0.006 0.077 821 Dihedral : 7.413 94.032 640 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.84 % Allowed : 21.71 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.21 (0.35), residues: 560 helix: -0.63 (0.31), residues: 272 sheet: -3.41 (1.08), residues: 17 loop : -2.24 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 58 HIS 0.006 0.001 HIS A 121 PHE 0.017 0.001 PHE A 266 TYR 0.027 0.001 TYR B 237 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8146 (pptt) cc_final: 0.7700 (pptt) REVERT: A 49 MET cc_start: 0.7398 (tpt) cc_final: 0.7101 (tpt) REVERT: A 57 TYR cc_start: 0.7782 (m-80) cc_final: 0.7376 (m-80) REVERT: A 62 GLN cc_start: 0.7385 (mp10) cc_final: 0.7100 (mp10) REVERT: A 106 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7917 (tp) REVERT: A 128 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7526 (mtm180) REVERT: A 150 LEU cc_start: 0.8322 (mp) cc_final: 0.7861 (mt) REVERT: A 154 ILE cc_start: 0.8427 (mt) cc_final: 0.8150 (mt) REVERT: A 233 SER cc_start: 0.8150 (p) cc_final: 0.7691 (m) REVERT: A 236 MET cc_start: 0.5825 (tmm) cc_final: 0.5172 (tmm) REVERT: A 270 MET cc_start: 0.7016 (mtm) cc_final: 0.6693 (mtm) REVERT: B 50 ARG cc_start: 0.7926 (mtt90) cc_final: 0.7495 (mpp-170) REVERT: B 122 LYS cc_start: 0.7879 (tptt) cc_final: 0.7550 (tptt) REVERT: B 196 LYS cc_start: 0.7650 (ptpp) cc_final: 0.7206 (ptpp) REVERT: B 246 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8025 (ttmm) outliers start: 25 outliers final: 15 residues processed: 152 average time/residue: 0.2400 time to fit residues: 44.1063 Evaluate side-chains 159 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.144477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128608 restraints weight = 7760.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132731 restraints weight = 3838.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135373 restraints weight = 2287.056| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4838 Z= 0.287 Angle : 0.750 8.341 6553 Z= 0.378 Chirality : 0.051 0.204 729 Planarity : 0.007 0.077 821 Dihedral : 7.326 82.078 640 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.88 % Allowed : 23.64 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.24 (0.35), residues: 560 helix: -0.64 (0.31), residues: 272 sheet: -3.71 (1.01), residues: 17 loop : -2.24 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 58 HIS 0.008 0.001 HIS A 121 PHE 0.015 0.002 PHE A 266 TYR 0.024 0.002 TYR B 237 ARG 0.003 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6656 (tt0) REVERT: A 12 LYS cc_start: 0.8205 (pptt) cc_final: 0.7826 (pptt) REVERT: A 37 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 49 MET cc_start: 0.7344 (tpt) cc_final: 0.7062 (tpt) REVERT: A 57 TYR cc_start: 0.7797 (m-80) cc_final: 0.7509 (m-80) REVERT: A 62 GLN cc_start: 0.7402 (mp10) cc_final: 0.7118 (mp10) REVERT: A 106 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 114 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7961 (mp) REVERT: A 128 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7298 (mtm180) REVERT: A 154 ILE cc_start: 0.8455 (mt) cc_final: 0.8200 (mt) REVERT: A 233 SER cc_start: 0.8377 (p) cc_final: 0.7943 (m) REVERT: A 270 MET cc_start: 0.6901 (mtm) cc_final: 0.6614 (mtm) REVERT: B 50 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7512 (mpp-170) REVERT: B 246 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8011 (ttmm) outliers start: 20 outliers final: 13 residues processed: 159 average time/residue: 0.2156 time to fit residues: 41.2918 Evaluate side-chains 161 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 11 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.131510 restraints weight = 7695.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135626 restraints weight = 3753.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138316 restraints weight = 2230.264| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4838 Z= 0.204 Angle : 0.718 7.464 6553 Z= 0.359 Chirality : 0.049 0.227 729 Planarity : 0.006 0.078 821 Dihedral : 7.138 80.695 640 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.07 % Allowed : 23.84 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.17 (0.35), residues: 560 helix: -0.61 (0.31), residues: 271 sheet: -3.77 (0.98), residues: 17 loop : -2.16 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 58 HIS 0.006 0.001 HIS A 127 PHE 0.022 0.001 PHE C 296 TYR 0.022 0.002 TYR B 237 ARG 0.005 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6639 (tt0) REVERT: A 12 LYS cc_start: 0.8183 (pptt) cc_final: 0.7785 (pptt) REVERT: A 49 MET cc_start: 0.7335 (tpt) cc_final: 0.7060 (tpt) REVERT: A 57 TYR cc_start: 0.7773 (m-80) cc_final: 0.7402 (m-80) REVERT: A 62 GLN cc_start: 0.7361 (mp10) cc_final: 0.7102 (mp10) REVERT: A 106 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 114 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7732 (mp) REVERT: A 128 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7376 (mtm180) REVERT: A 154 ILE cc_start: 0.8413 (mt) cc_final: 0.8168 (mt) REVERT: A 170 TYR cc_start: 0.7858 (m-80) cc_final: 0.7524 (m-80) REVERT: A 233 SER cc_start: 0.8341 (p) cc_final: 0.7917 (m) REVERT: A 270 MET cc_start: 0.6875 (mtm) cc_final: 0.6653 (mtm) REVERT: B 50 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7529 (mpp-170) REVERT: B 114 LEU cc_start: 0.7965 (pp) cc_final: 0.7747 (mt) REVERT: B 119 PHE cc_start: 0.7710 (t80) cc_final: 0.7422 (t80) REVERT: B 122 LYS cc_start: 0.7879 (tptt) cc_final: 0.7569 (tptt) REVERT: B 216 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7720 (mttt) REVERT: B 246 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7982 (ttmm) outliers start: 21 outliers final: 13 residues processed: 146 average time/residue: 0.2032 time to fit residues: 35.9453 Evaluate side-chains 149 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 58 TRP Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 0.0770 chunk 33 optimal weight: 0.0170 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 42 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 overall best weight: 0.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134754 restraints weight = 7733.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138936 restraints weight = 3810.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141610 restraints weight = 2271.008| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4838 Z= 0.179 Angle : 0.699 6.601 6553 Z= 0.348 Chirality : 0.048 0.192 729 Planarity : 0.006 0.078 821 Dihedral : 6.189 77.440 640 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.71 % Allowed : 26.55 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.36), residues: 560 helix: -0.68 (0.31), residues: 283 sheet: -3.81 (1.00), residues: 17 loop : -2.16 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 58 HIS 0.004 0.001 HIS A 127 PHE 0.021 0.001 PHE C 296 TYR 0.021 0.001 TYR B 237 ARG 0.002 0.000 ARG B 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.8170 (pptt) cc_final: 0.7722 (pptt) REVERT: A 49 MET cc_start: 0.7386 (tpt) cc_final: 0.7107 (tpt) REVERT: A 57 TYR cc_start: 0.7681 (m-80) cc_final: 0.7291 (m-80) REVERT: A 106 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7986 (tp) REVERT: A 128 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7424 (mtm180) REVERT: A 154 ILE cc_start: 0.8385 (mt) cc_final: 0.8129 (mt) REVERT: A 170 TYR cc_start: 0.7828 (m-80) cc_final: 0.7571 (m-80) REVERT: A 233 SER cc_start: 0.8247 (p) cc_final: 0.7872 (m) REVERT: B 50 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7506 (mpp-170) REVERT: B 114 LEU cc_start: 0.7967 (pp) cc_final: 0.7728 (mt) REVERT: B 122 LYS cc_start: 0.7867 (tptt) cc_final: 0.7529 (tptt) REVERT: B 216 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7724 (mttt) REVERT: B 246 LYS cc_start: 0.8361 (ttmm) cc_final: 0.7996 (ttmm) outliers start: 14 outliers final: 11 residues processed: 150 average time/residue: 0.2126 time to fit residues: 39.1019 Evaluate side-chains 160 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 58 TRP Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132431 restraints weight = 7793.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136606 restraints weight = 3790.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139389 restraints weight = 2234.808| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4838 Z= 0.215 Angle : 0.728 7.319 6553 Z= 0.363 Chirality : 0.049 0.199 729 Planarity : 0.006 0.078 821 Dihedral : 5.964 75.677 640 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.13 % Allowed : 27.91 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.36), residues: 560 helix: -0.58 (0.32), residues: 277 sheet: -3.85 (1.02), residues: 17 loop : -2.20 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.021 0.001 PHE C 296 TYR 0.021 0.001 TYR B 237 ARG 0.004 0.000 ARG B 248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.58 seconds wall clock time: 41 minutes 9.69 seconds (2469.69 seconds total)