Starting phenix.real_space_refine on Tue Feb 11 15:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7voj_32050/02_2025/7voj_32050.cif Found real_map, /net/cci-nas-00/data/ceres_data/7voj_32050/02_2025/7voj_32050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7voj_32050/02_2025/7voj_32050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7voj_32050/02_2025/7voj_32050.map" model { file = "/net/cci-nas-00/data/ceres_data/7voj_32050/02_2025/7voj_32050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7voj_32050/02_2025/7voj_32050.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 16 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: 5 Type Number sf(0) Gaussians Al 2 5.89 5 S 32 5.16 5 C 4074 2.51 5 N 1052 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6318 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3150 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' AL': 1, 'ACY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.08, per 1000 atoms: 0.80 Number of scatterers: 6318 At special positions: 0 Unit cell: (84.162, 84.162, 113.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 Al 2 13.00 O 1158 8.00 N 1052 7.00 C 4074 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: 1.54 Conformation dependent library (CDL) restraints added in 936.8 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.753A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 42 removed outlier: 3.723A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.879A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 102 removed outlier: 3.844A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 156 through 183 Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.754A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.716A pdb=" N GLU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.750A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.727A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.914A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 399 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.753A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 42 removed outlier: 3.723A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.879A pdb=" N VAL B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 102 removed outlier: 3.844A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 156 through 183 Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.754A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.716A pdb=" N GLU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.750A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.727A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.914A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 399 521 hydrogen bonds defined for protein. 1563 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: 1.81 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1610 1.33 - 1.45: 1186 1.45 - 1.57: 3588 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6440 Sorted by residual: bond pdb=" C CYS A 184 " pdb=" O CYS A 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C CYS B 184 " pdb=" O CYS B 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C GLY A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" C GLY B 102 " pdb=" N ALA B 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" CA TYR B 50 " pdb=" C TYR B 50 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.37e-02 5.33e+03 3.59e+00 ... (remaining 6435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 8322 2.18 - 4.36: 328 4.36 - 6.54: 24 6.54 - 8.72: 18 8.72 - 10.90: 6 Bond angle restraints: 8698 Sorted by residual: angle pdb=" N PHE B 51 " pdb=" CA PHE B 51 " pdb=" C PHE B 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE A 51 " pdb=" CA PHE A 51 " pdb=" C PHE A 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE B 182 " pdb=" CA PHE B 182 " pdb=" C PHE B 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N PHE A 182 " pdb=" CA PHE A 182 " pdb=" C PHE A 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 110.62 117.44 -6.82 1.02e+00 9.61e-01 4.48e+01 ... (remaining 8693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 3354 14.31 - 28.62: 372 28.62 - 42.93: 88 42.93 - 57.24: 30 57.24 - 71.55: 6 Dihedral angle restraints: 3850 sinusoidal: 1526 harmonic: 2324 Sorted by residual: dihedral pdb=" CA ARG B 154 " pdb=" C ARG B 154 " pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG A 154 " pdb=" C ARG A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 866 0.081 - 0.162: 110 0.162 - 0.243: 14 0.243 - 0.324: 2 0.324 - 0.404: 4 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PHE B 182 " pdb=" N PHE B 182 " pdb=" C PHE B 182 " pdb=" CB PHE B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 182 " pdb=" N PHE A 182 " pdb=" C PHE A 182 " pdb=" CB PHE A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 51 " pdb=" N PHE A 51 " pdb=" C PHE A 51 " pdb=" CB PHE A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 993 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 180 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER B 180 " -0.068 2.00e-02 2.50e+03 pdb=" O SER B 180 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE B 181 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 180 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 180 " 0.068 2.00e-02 2.50e+03 pdb=" O SER A 180 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 181 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 184 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO B 185 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.042 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 96 2.63 - 3.20: 5470 3.20 - 3.76: 9637 3.76 - 4.33: 12737 4.33 - 4.90: 21603 Nonbonded interactions: 49543 Sorted by model distance: nonbonded pdb=" OD1 ASP A 160 " pdb="AL AL A 603 " model vdw 2.061 2.020 nonbonded pdb=" OD1 ASP B 160 " pdb="AL AL B 603 " model vdw 2.061 2.020 nonbonded pdb=" OD2 ASP B 160 " pdb="AL AL B 603 " model vdw 2.113 2.020 nonbonded pdb=" OD2 ASP A 160 " pdb="AL AL A 603 " model vdw 2.113 2.020 nonbonded pdb=" O ACY B 601 " pdb="AL AL B 603 " model vdw 2.116 2.020 ... (remaining 49538 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.780 Find NCS groups from input model: 0.120 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.008 0.057 6440 Z= 0.529 Angle : 1.008 10.902 8698 Z= 0.626 Chirality : 0.062 0.404 996 Planarity : 0.007 0.071 1094 Dihedral : 13.588 71.548 2346 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 1.73 % Allowed : 12.39 % Favored : 85.88 % 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: -2.46 (0.26), residues: 792 helix: -1.27 (0.17), residues: 664 sheet: None (None), residues: 0 loop : -2.54 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 129 HIS 0.003 0.001 HIS A 340 PHE 0.016 0.002 PHE B 134 TYR 0.015 0.002 TYR A 236 ARG 0.003 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.661 Fit side-chains REVERT: A 5 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.5751 (mmp-170) REVERT: A 96 GLN cc_start: 0.7767 (mm110) cc_final: 0.7501 (mm-40) REVERT: A 201 ASP cc_start: 0.7736 (t0) cc_final: 0.7447 (t70) REVERT: A 209 ASP cc_start: 0.7532 (m-30) cc_final: 0.7159 (m-30) REVERT: A 226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p) REVERT: A 370 SER cc_start: 0.9002 (m) cc_final: 0.8750 (p) REVERT: B 5 ARG cc_start: 0.6463 (mtt-85) cc_final: 0.5741 (mmp-170) REVERT: B 96 GLN cc_start: 0.7758 (mm110) cc_final: 0.7491 (mm-40) REVERT: B 201 ASP cc_start: 0.7733 (t0) cc_final: 0.7444 (t70) REVERT: B 209 ASP cc_start: 0.7539 (m-30) cc_final: 0.7165 (m-30) REVERT: B 226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p) outliers start: 12 outliers final: 10 residues processed: 149 average time/residue: 1.0616 time to fit residues: 166.7817 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 96 GLN A 266 HIS A 289 ASN A 293 ASN A 330 GLN A 403 ASN B 24 HIS B 96 GLN B 266 HIS B 289 ASN B 293 ASN B 330 GLN B 403 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.160873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111650 restraints weight = 7430.310| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.20 r_work: 0.3181 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6440 Z= 0.174 Angle : 0.533 5.749 8698 Z= 0.295 Chirality : 0.037 0.137 996 Planarity : 0.004 0.042 1094 Dihedral : 5.671 55.926 874 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.88 % Allowed : 19.74 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 792 helix: 1.27 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.65 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 129 HIS 0.004 0.001 HIS B 193 PHE 0.020 0.001 PHE A 206 TYR 0.011 0.001 TYR B 50 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.658 Fit side-chains REVERT: A 5 ARG cc_start: 0.6552 (mtt-85) cc_final: 0.5966 (mmp-170) REVERT: A 201 ASP cc_start: 0.8108 (t0) cc_final: 0.7848 (t70) REVERT: A 209 ASP cc_start: 0.7347 (m-30) cc_final: 0.6947 (m-30) REVERT: A 265 ARG cc_start: 0.7209 (mmt180) cc_final: 0.6990 (tpp80) REVERT: B 5 ARG cc_start: 0.6491 (mtt-85) cc_final: 0.5601 (mmp-170) REVERT: B 201 ASP cc_start: 0.8114 (t0) cc_final: 0.7854 (t70) REVERT: B 209 ASP cc_start: 0.7358 (m-30) cc_final: 0.6955 (m-30) REVERT: B 265 ARG cc_start: 0.7193 (mmt180) cc_final: 0.6956 (tpp80) outliers start: 20 outliers final: 8 residues processed: 121 average time/residue: 0.9722 time to fit residues: 124.9060 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** 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 = 0.3933 r_free = 0.3933 target = 0.163384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112906 restraints weight = 7416.723| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.29 r_work: 0.3146 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6440 Z= 0.151 Angle : 0.482 5.943 8698 Z= 0.257 Chirality : 0.035 0.140 996 Planarity : 0.003 0.043 1094 Dihedral : 4.728 54.238 862 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.60 % Allowed : 20.32 % Favored : 76.08 % 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: 2.42 (0.31), residues: 792 helix: 2.38 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.53 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 129 HIS 0.002 0.000 HIS B 193 PHE 0.016 0.001 PHE A 206 TYR 0.010 0.001 TYR B 50 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.746 Fit side-chains REVERT: A 5 ARG cc_start: 0.6794 (mtt-85) cc_final: 0.5860 (mmp-170) REVERT: A 129 TRP cc_start: 0.7187 (t-100) cc_final: 0.6976 (t60) REVERT: A 201 ASP cc_start: 0.7991 (t0) cc_final: 0.7693 (t70) REVERT: A 209 ASP cc_start: 0.7305 (m-30) cc_final: 0.6809 (m-30) REVERT: A 265 ARG cc_start: 0.7149 (mmt180) cc_final: 0.6845 (tpp80) REVERT: B 5 ARG cc_start: 0.6488 (mtt-85) cc_final: 0.5859 (mmp-170) REVERT: B 129 TRP cc_start: 0.7176 (t-100) cc_final: 0.6964 (t60) REVERT: B 201 ASP cc_start: 0.7991 (t0) cc_final: 0.7707 (t0) REVERT: B 209 ASP cc_start: 0.7257 (m-30) cc_final: 0.6766 (m-30) REVERT: B 265 ARG cc_start: 0.7152 (mmt180) cc_final: 0.6844 (tpp80) outliers start: 25 outliers final: 6 residues processed: 121 average time/residue: 1.0120 time to fit residues: 129.8772 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 293 ASN B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097110 restraints weight = 7754.878| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.20 r_work: 0.2990 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6440 Z= 0.327 Angle : 0.582 5.450 8698 Z= 0.317 Chirality : 0.039 0.145 996 Planarity : 0.004 0.043 1094 Dihedral : 4.569 36.128 862 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.75 % Allowed : 22.33 % Favored : 73.92 % 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: 2.31 (0.31), residues: 792 helix: 2.36 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.82 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 129 HIS 0.005 0.001 HIS A 193 PHE 0.011 0.002 PHE B 141 TYR 0.011 0.002 TYR B 39 ARG 0.008 0.001 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.726 Fit side-chains REVERT: A 5 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6282 (mmp-170) REVERT: A 201 ASP cc_start: 0.8109 (t0) cc_final: 0.7796 (t70) REVERT: A 209 ASP cc_start: 0.7596 (m-30) cc_final: 0.7198 (m-30) REVERT: A 265 ARG cc_start: 0.7210 (mmt180) cc_final: 0.6869 (tpp80) REVERT: A 334 SER cc_start: 0.8598 (m) cc_final: 0.8334 (p) REVERT: B 5 ARG cc_start: 0.7101 (mtt-85) cc_final: 0.6279 (mmp-170) REVERT: B 201 ASP cc_start: 0.8111 (t0) cc_final: 0.7800 (t70) REVERT: B 209 ASP cc_start: 0.7600 (m-30) cc_final: 0.7205 (m-30) REVERT: B 265 ARG cc_start: 0.7202 (mmt180) cc_final: 0.6858 (tpp80) REVERT: B 334 SER cc_start: 0.8596 (m) cc_final: 0.8333 (p) outliers start: 26 outliers final: 8 residues processed: 121 average time/residue: 0.9517 time to fit residues: 122.6814 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 376 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 293 ASN B 266 HIS B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103614 restraints weight = 7535.450| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.20 r_work: 0.3112 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6440 Z= 0.165 Angle : 0.493 6.113 8698 Z= 0.266 Chirality : 0.036 0.138 996 Planarity : 0.003 0.041 1094 Dihedral : 4.083 18.647 862 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.74 % Allowed : 24.21 % Favored : 73.05 % 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: 2.81 (0.30), residues: 792 helix: 2.70 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.74 (0.48), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 129 HIS 0.003 0.001 HIS B 193 PHE 0.013 0.001 PHE A 206 TYR 0.013 0.001 TYR B 50 ARG 0.007 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.656 Fit side-chains REVERT: A 5 ARG cc_start: 0.7031 (mtt-85) cc_final: 0.6236 (mmp-170) REVERT: A 7 ILE cc_start: 0.8129 (tt) cc_final: 0.7823 (mt) REVERT: A 129 TRP cc_start: 0.7077 (t-100) cc_final: 0.6825 (t60) REVERT: A 201 ASP cc_start: 0.8107 (t0) cc_final: 0.7790 (t70) REVERT: A 209 ASP cc_start: 0.7445 (m-30) cc_final: 0.6963 (m-30) REVERT: A 265 ARG cc_start: 0.7362 (mmt180) cc_final: 0.7055 (tpp80) REVERT: A 291 TYR cc_start: 0.8188 (t80) cc_final: 0.7899 (t80) REVERT: A 334 SER cc_start: 0.8641 (m) cc_final: 0.8369 (p) REVERT: B 5 ARG cc_start: 0.7078 (mtt-85) cc_final: 0.6267 (mmp-170) REVERT: B 129 TRP cc_start: 0.7036 (t-100) cc_final: 0.6784 (t60) REVERT: B 201 ASP cc_start: 0.8112 (t0) cc_final: 0.7795 (t70) REVERT: B 209 ASP cc_start: 0.7409 (m-30) cc_final: 0.6949 (m-30) REVERT: B 265 ARG cc_start: 0.7328 (mmt180) cc_final: 0.7017 (tpp80) REVERT: B 291 TYR cc_start: 0.8206 (t80) cc_final: 0.7919 (t80) REVERT: B 334 SER cc_start: 0.8632 (m) cc_final: 0.8361 (p) outliers start: 19 outliers final: 11 residues processed: 112 average time/residue: 0.9312 time to fit residues: 110.8378 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104518 restraints weight = 7521.466| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.19 r_work: 0.3106 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6440 Z= 0.166 Angle : 0.512 7.782 8698 Z= 0.268 Chirality : 0.036 0.128 996 Planarity : 0.003 0.039 1094 Dihedral : 3.898 18.473 858 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.31 % Allowed : 24.93 % Favored : 71.76 % 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: 3.04 (0.30), residues: 792 helix: 2.85 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.70 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.003 0.001 HIS A 193 PHE 0.011 0.001 PHE B 206 TYR 0.007 0.001 TYR A 236 ARG 0.008 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.634 Fit side-chains REVERT: A 5 ARG cc_start: 0.7055 (mtt-85) cc_final: 0.6300 (mmp-170) REVERT: A 7 ILE cc_start: 0.8139 (tt) cc_final: 0.7834 (mt) REVERT: A 129 TRP cc_start: 0.7021 (t-100) cc_final: 0.6773 (t60) REVERT: A 201 ASP cc_start: 0.8125 (t0) cc_final: 0.7914 (t0) REVERT: A 209 ASP cc_start: 0.7459 (m-30) cc_final: 0.6940 (m-30) REVERT: A 265 ARG cc_start: 0.7312 (mmt180) cc_final: 0.7026 (tpp80) REVERT: A 291 TYR cc_start: 0.8077 (t80) cc_final: 0.7785 (t80) REVERT: A 334 SER cc_start: 0.8630 (m) cc_final: 0.8402 (p) REVERT: A 402 LYS cc_start: 0.8445 (pttt) cc_final: 0.8236 (pttt) REVERT: B 5 ARG cc_start: 0.7067 (mtt-85) cc_final: 0.6320 (mmp-170) REVERT: B 7 ILE cc_start: 0.8144 (tt) cc_final: 0.7841 (mt) REVERT: B 129 TRP cc_start: 0.7000 (t-100) cc_final: 0.6752 (t60) REVERT: B 201 ASP cc_start: 0.8124 (t0) cc_final: 0.7808 (t70) REVERT: B 209 ASP cc_start: 0.7461 (m-30) cc_final: 0.6939 (m-30) REVERT: B 265 ARG cc_start: 0.7311 (mmt180) cc_final: 0.7020 (tpp80) REVERT: B 291 TYR cc_start: 0.8098 (t80) cc_final: 0.7801 (t80) REVERT: B 334 SER cc_start: 0.8617 (m) cc_final: 0.8393 (p) REVERT: B 402 LYS cc_start: 0.8437 (pttt) cc_final: 0.8221 (pttt) outliers start: 23 outliers final: 16 residues processed: 115 average time/residue: 0.9571 time to fit residues: 116.9620 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 51 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103369 restraints weight = 7625.504| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.23 r_work: 0.3049 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6440 Z= 0.180 Angle : 0.510 7.956 8698 Z= 0.271 Chirality : 0.036 0.129 996 Planarity : 0.003 0.039 1094 Dihedral : 3.900 18.441 858 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.88 % Allowed : 26.08 % Favored : 71.04 % 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 (0.30), residues: 792 helix: 2.91 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -2.77 (0.47), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS A 193 PHE 0.012 0.001 PHE A 206 TYR 0.014 0.001 TYR B 50 ARG 0.007 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.777 Fit side-chains REVERT: A 5 ARG cc_start: 0.7074 (mtt-85) cc_final: 0.6299 (mmp-170) REVERT: A 7 ILE cc_start: 0.8067 (tt) cc_final: 0.7752 (mt) REVERT: A 129 TRP cc_start: 0.6997 (t-100) cc_final: 0.6729 (t60) REVERT: A 201 ASP cc_start: 0.8080 (t0) cc_final: 0.7858 (t0) REVERT: A 209 ASP cc_start: 0.7442 (m-30) cc_final: 0.6935 (m-30) REVERT: A 265 ARG cc_start: 0.7358 (mmt180) cc_final: 0.7056 (tpp80) REVERT: A 291 TYR cc_start: 0.8095 (t80) cc_final: 0.7845 (t80) REVERT: A 334 SER cc_start: 0.8600 (m) cc_final: 0.8392 (p) REVERT: B 5 ARG cc_start: 0.7062 (mtt-85) cc_final: 0.6327 (mmp-170) REVERT: B 7 ILE cc_start: 0.8060 (tt) cc_final: 0.7762 (mt) REVERT: B 129 TRP cc_start: 0.6994 (t-100) cc_final: 0.6732 (t60) REVERT: B 201 ASP cc_start: 0.8110 (t0) cc_final: 0.7802 (t70) REVERT: B 209 ASP cc_start: 0.7436 (m-30) cc_final: 0.6922 (m-30) REVERT: B 265 ARG cc_start: 0.7366 (mmt180) cc_final: 0.7047 (tpp80) REVERT: B 291 TYR cc_start: 0.8073 (t80) cc_final: 0.7789 (t80) REVERT: B 334 SER cc_start: 0.8598 (m) cc_final: 0.8392 (p) outliers start: 20 outliers final: 17 residues processed: 116 average time/residue: 1.0380 time to fit residues: 127.7789 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 0.0020 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.156095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106558 restraints weight = 7481.381| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.19 r_work: 0.3091 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6440 Z= 0.157 Angle : 0.513 8.861 8698 Z= 0.267 Chirality : 0.035 0.129 996 Planarity : 0.003 0.039 1094 Dihedral : 3.819 18.246 858 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.31 % Allowed : 27.09 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.30), residues: 792 helix: 3.06 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -2.69 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 129 HIS 0.002 0.001 HIS A 193 PHE 0.009 0.001 PHE A 206 TYR 0.008 0.001 TYR A 236 ARG 0.008 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.744 Fit side-chains REVERT: A 5 ARG cc_start: 0.7109 (mtt-85) cc_final: 0.6319 (mmp-170) REVERT: A 7 ILE cc_start: 0.8065 (tt) cc_final: 0.7744 (mt) REVERT: A 129 TRP cc_start: 0.6726 (t-100) cc_final: 0.6454 (t60) REVERT: A 201 ASP cc_start: 0.8052 (t0) cc_final: 0.7840 (t0) REVERT: A 209 ASP cc_start: 0.7407 (m-30) cc_final: 0.6847 (m-30) REVERT: A 265 ARG cc_start: 0.7385 (mmt180) cc_final: 0.7072 (tpp80) REVERT: A 291 TYR cc_start: 0.7956 (t80) cc_final: 0.7694 (t80) REVERT: A 334 SER cc_start: 0.8602 (m) cc_final: 0.8375 (p) REVERT: B 5 ARG cc_start: 0.7041 (mtt-85) cc_final: 0.6141 (mmp-170) REVERT: B 7 ILE cc_start: 0.8068 (tt) cc_final: 0.7771 (mt) REVERT: B 129 TRP cc_start: 0.6709 (t-100) cc_final: 0.6431 (t60) REVERT: B 201 ASP cc_start: 0.8076 (t0) cc_final: 0.7870 (t0) REVERT: B 209 ASP cc_start: 0.7408 (m-30) cc_final: 0.6850 (m-30) REVERT: B 265 ARG cc_start: 0.7390 (mmt180) cc_final: 0.7074 (tpp80) REVERT: B 291 TYR cc_start: 0.7951 (t80) cc_final: 0.7656 (t80) REVERT: B 334 SER cc_start: 0.8585 (m) cc_final: 0.8359 (p) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 1.0660 time to fit residues: 131.0307 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.154445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105318 restraints weight = 7528.091| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.16 r_work: 0.3054 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.041 6440 Z= 0.202 Angle : 0.545 8.819 8698 Z= 0.286 Chirality : 0.036 0.132 996 Planarity : 0.004 0.065 1094 Dihedral : 3.916 18.105 858 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.02 % Allowed : 28.39 % Favored : 69.60 % 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: 3.18 (0.30), residues: 792 helix: 2.99 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -2.82 (0.47), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.003 0.001 HIS B 193 PHE 0.014 0.001 PHE A 264 TYR 0.016 0.002 TYR B 50 ARG 0.015 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.640 Fit side-chains REVERT: A 5 ARG cc_start: 0.7103 (mtt-85) cc_final: 0.6346 (mmp-170) REVERT: A 7 ILE cc_start: 0.8091 (tt) cc_final: 0.7775 (mt) REVERT: A 129 TRP cc_start: 0.6966 (t-100) cc_final: 0.6718 (t60) REVERT: A 201 ASP cc_start: 0.8057 (t0) cc_final: 0.7844 (t0) REVERT: A 209 ASP cc_start: 0.7408 (m-30) cc_final: 0.6872 (m-30) REVERT: A 265 ARG cc_start: 0.7445 (mmt180) cc_final: 0.7122 (tpp80) REVERT: A 291 TYR cc_start: 0.7960 (t80) cc_final: 0.7717 (t80) REVERT: B 5 ARG cc_start: 0.7096 (mtt-85) cc_final: 0.6326 (mmp-170) REVERT: B 7 ILE cc_start: 0.8103 (tt) cc_final: 0.7802 (mt) REVERT: B 129 TRP cc_start: 0.6942 (t-100) cc_final: 0.6684 (t60) REVERT: B 201 ASP cc_start: 0.8072 (t0) cc_final: 0.7865 (t0) REVERT: B 209 ASP cc_start: 0.7409 (m-30) cc_final: 0.6866 (m-30) REVERT: B 265 ARG cc_start: 0.7447 (mmt180) cc_final: 0.7127 (tpp80) REVERT: B 291 TYR cc_start: 0.7940 (t80) cc_final: 0.7696 (t80) outliers start: 14 outliers final: 13 residues processed: 110 average time/residue: 1.0589 time to fit residues: 123.8091 Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.155399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106267 restraints weight = 7546.024| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.17 r_work: 0.3065 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6440 Z= 0.191 Angle : 0.548 9.957 8698 Z= 0.287 Chirality : 0.036 0.123 996 Planarity : 0.003 0.037 1094 Dihedral : 3.888 18.191 858 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 28.24 % Favored : 69.60 % 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: 3.24 (0.30), residues: 792 helix: 3.01 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -2.74 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS B 193 PHE 0.014 0.001 PHE A 206 TYR 0.008 0.001 TYR A 236 ARG 0.008 0.000 ARG B 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.696 Fit side-chains REVERT: A 5 ARG cc_start: 0.7099 (mtt-85) cc_final: 0.6278 (mmp-170) REVERT: A 7 ILE cc_start: 0.8090 (tt) cc_final: 0.7746 (mt) REVERT: A 129 TRP cc_start: 0.6879 (t-100) cc_final: 0.6615 (t60) REVERT: A 201 ASP cc_start: 0.8058 (t0) cc_final: 0.7845 (t0) REVERT: A 209 ASP cc_start: 0.7408 (m-30) cc_final: 0.6897 (m-30) REVERT: A 265 ARG cc_start: 0.7448 (mmt180) cc_final: 0.7139 (tpp80) REVERT: A 291 TYR cc_start: 0.7937 (t80) cc_final: 0.7691 (t80) REVERT: B 5 ARG cc_start: 0.7072 (mtt-85) cc_final: 0.6455 (mmp-170) REVERT: B 7 ILE cc_start: 0.8102 (tt) cc_final: 0.7805 (mt) REVERT: B 129 TRP cc_start: 0.6877 (t-100) cc_final: 0.6610 (t60) REVERT: B 201 ASP cc_start: 0.8127 (t0) cc_final: 0.7918 (t0) REVERT: B 209 ASP cc_start: 0.7408 (m-30) cc_final: 0.6893 (m-30) REVERT: B 265 ARG cc_start: 0.7442 (mmt180) cc_final: 0.7127 (tpp80) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 1.0192 time to fit residues: 119.8651 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.151764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102167 restraints weight = 7672.085| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.18 r_work: 0.3024 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6440 Z= 0.213 Angle : 0.567 10.040 8698 Z= 0.296 Chirality : 0.036 0.124 996 Planarity : 0.004 0.069 1094 Dihedral : 3.977 18.179 858 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.74 % Allowed : 27.38 % Favored : 69.88 % 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: 3.13 (0.30), residues: 792 helix: 2.96 (0.19), residues: 656 sheet: None (None), residues: 0 loop : -2.87 (0.46), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 255 HIS 0.004 0.001 HIS B 193 PHE 0.018 0.001 PHE A 264 TYR 0.016 0.002 TYR B 50 ARG 0.015 0.000 ARG A 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4974.45 seconds wall clock time: 88 minutes 19.26 seconds (5299.26 seconds total)