Starting phenix.real_space_refine on Wed Mar 5 21:25:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xd6_38267/03_2025/8xd6_38267_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xd6_38267/03_2025/8xd6_38267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xd6_38267/03_2025/8xd6_38267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xd6_38267/03_2025/8xd6_38267.map" model { file = "/net/cci-nas-00/data/ceres_data/8xd6_38267/03_2025/8xd6_38267_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xd6_38267/03_2025/8xd6_38267_neut.cif" } resolution = 2.79 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 15 5.16 5 C 2131 2.51 5 N 568 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3402 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3289 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 113 Unusual residues: {'AKG': 2, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 4, 'water': 44} Link IDs: {None: 47} Time building chain proxies: 2.90, per 1000 atoms: 0.85 Number of scatterers: 3402 At special positions: 0 Unit cell: (67.68, 75.952, 69.184, 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 15 16.00 P 3 15.00 O 685 8.00 N 568 7.00 C 2131 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: 0.96 Conformation dependent library (CDL) restraints added in 417.2 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 55.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.814A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.918A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.512A pdb=" N ILE A 309 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.427A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 415 removed outlier: 3.762A pdb=" N SER A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.652A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 6.470A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 243 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 570 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: 1.00 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1033 1.34 - 1.45: 461 1.45 - 1.57: 1907 1.57 - 1.69: 2 1.69 - 1.80: 29 Bond restraints: 3432 Sorted by residual: bond pdb=" O1N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.477 1.549 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.566 0.267 3.80e-02 6.93e+02 4.93e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.558 0.199 3.50e-02 8.16e+02 3.23e+01 bond pdb=" C1 AKG A 503 " pdb=" C2 AKG A 503 " ideal model delta sigma weight residual 1.559 1.460 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C1 AKG A 502 " pdb=" C2 AKG A 502 " ideal model delta sigma weight residual 1.559 1.462 0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 4614 4.43 - 8.86: 27 8.86 - 13.28: 13 13.28 - 17.71: 4 17.71 - 22.14: 1 Bond angle restraints: 4659 Sorted by residual: angle pdb=" C1D NDP A 501 " pdb=" O4D NDP A 501 " pdb=" C4D NDP A 501 " ideal model delta sigma weight residual 105.41 127.55 -22.14 2.71e+00 1.37e-01 6.69e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.22 -15.38 1.91e+00 2.73e-01 6.45e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 122.54 -14.80 1.95e+00 2.62e-01 5.74e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 109.41 8.05 1.17e+00 7.36e-01 4.76e+01 angle pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.33 108.87 8.46 1.48e+00 4.57e-01 3.28e+01 ... (remaining 4654 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 30.96: 1948 30.96 - 61.91: 75 61.91 - 92.86: 9 92.86 - 123.81: 0 123.81 - 154.76: 1 Dihedral angle restraints: 2033 sinusoidal: 835 harmonic: 1198 Sorted by residual: dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 20.28 154.76 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CB GLU A 371 " pdb=" CG GLU A 371 " pdb=" CD GLU A 371 " pdb=" OE1 GLU A 371 " ideal model delta sinusoidal sigma weight residual 0.00 -84.13 84.13 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 447 0.079 - 0.159: 50 0.159 - 0.238: 2 0.238 - 0.318: 3 0.318 - 0.397: 3 Chirality restraints: 505 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.32 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C1B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" N9A NDP A 501 " pdb=" O4B NDP A 501 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 502 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.103 2.00e-02 2.50e+03 1.98e-01 3.90e+02 pdb=" C5N NDP A 501 " 0.255 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.261 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " 0.058 2.00e-02 2.50e+03 1.01e-01 1.26e+02 pdb=" C3N NDP A 501 " 0.167 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.039 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " -0.106 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 297 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C ILE A 297 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 297 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 298 " 0.017 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1239 2.88 - 3.38: 3313 3.38 - 3.89: 6137 3.89 - 4.39: 7345 4.39 - 4.90: 11813 Nonbonded interactions: 29847 Sorted by model distance: nonbonded pdb=" O LEU A 99 " pdb=" O HOH A 601 " model vdw 2.369 3.040 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.447 3.120 nonbonded pdb=" O GLU A 286 " pdb=" NZ LYS A 310 " model vdw 2.464 3.120 nonbonded pdb=" N ASN A 222 " pdb=" O2A NDP A 501 " model vdw 2.482 3.120 nonbonded pdb=" NE ARG A 58 " pdb=" OD2 ASP A 140 " model vdw 2.500 3.120 ... (remaining 29842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.030 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 : 0.009 0.267 3432 Z= 0.537 Angle : 1.123 22.139 4659 Z= 0.569 Chirality : 0.058 0.397 505 Planarity : 0.010 0.198 596 Dihedral : 16.233 154.763 1269 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.51 % Allowed : 2.92 % Favored : 93.57 % 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: 0.89 (0.43), residues: 417 helix: 1.30 (0.37), residues: 210 sheet: 0.53 (0.74), residues: 60 loop : -0.31 (0.55), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 63 HIS 0.003 0.001 HIS A 61 PHE 0.009 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.397 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 1.5859 time to fit residues: 111.9326 Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.085790 restraints weight = 4398.787| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 1.51 r_work: 0.2580 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3432 Z= 0.233 Angle : 0.488 4.240 4659 Z= 0.259 Chirality : 0.043 0.137 505 Planarity : 0.004 0.041 596 Dihedral : 10.388 148.402 485 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.05 % Allowed : 9.94 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.43), residues: 417 helix: 1.93 (0.36), residues: 210 sheet: 0.53 (0.73), residues: 61 loop : -0.24 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.002 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.425 Fit side-chains REVERT: A 1 MET cc_start: 0.6209 (tpp) cc_final: 0.5635 (tpp) REVERT: A 16 ARG cc_start: 0.8788 (ttt90) cc_final: 0.8252 (ttm170) REVERT: A 113 LYS cc_start: 0.9318 (mmtm) cc_final: 0.8932 (mttp) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 1.6995 time to fit residues: 100.9153 Evaluate side-chains 55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.0040 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.085592 restraints weight = 4361.001| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.47 r_work: 0.2582 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3432 Z= 0.252 Angle : 0.482 4.174 4659 Z= 0.256 Chirality : 0.043 0.134 505 Planarity : 0.004 0.042 596 Dihedral : 9.658 146.238 478 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.05 % Allowed : 11.11 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.43), residues: 417 helix: 1.90 (0.36), residues: 212 sheet: 0.50 (0.73), residues: 61 loop : -0.13 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.005 0.002 HIS A 388 PHE 0.013 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.434 Fit side-chains REVERT: A 1 MET cc_start: 0.6158 (tpp) cc_final: 0.5574 (tpp) REVERT: A 16 ARG cc_start: 0.8754 (ttt90) cc_final: 0.8298 (ttm170) REVERT: A 60 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.9117 (mt0) REVERT: A 113 LYS cc_start: 0.9300 (mmtm) cc_final: 0.8927 (mttp) REVERT: A 118 ARG cc_start: 0.8708 (mmp80) cc_final: 0.8486 (mmp80) outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 1.7467 time to fit residues: 94.7686 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.074430 restraints weight = 4521.436| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 1.59 r_work: 0.2497 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3432 Z= 0.362 Angle : 0.503 4.207 4659 Z= 0.268 Chirality : 0.045 0.131 505 Planarity : 0.004 0.046 596 Dihedral : 9.066 140.165 478 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.75 % Allowed : 12.57 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.43), residues: 417 helix: 1.87 (0.36), residues: 207 sheet: 0.47 (0.73), residues: 61 loop : -0.38 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.007 0.002 HIS A 388 PHE 0.016 0.002 PHE A 341 TYR 0.016 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.413 Fit side-chains REVERT: A 1 MET cc_start: 0.6183 (tpp) cc_final: 0.5649 (tpp) REVERT: A 16 ARG cc_start: 0.8694 (ttt90) cc_final: 0.8135 (ttm170) REVERT: A 113 LYS cc_start: 0.9315 (mmtm) cc_final: 0.8909 (mttp) REVERT: A 312 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8620 (mttp) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 1.8793 time to fit residues: 101.8861 Evaluate side-chains 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.078723 restraints weight = 4522.848| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.58 r_work: 0.2592 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3432 Z= 0.226 Angle : 0.455 3.966 4659 Z= 0.244 Chirality : 0.043 0.132 505 Planarity : 0.004 0.048 596 Dihedral : 8.659 135.444 475 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.75 % Allowed : 12.87 % Favored : 85.38 % 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: 1.40 (0.43), residues: 417 helix: 2.00 (0.36), residues: 207 sheet: 0.43 (0.72), residues: 61 loop : -0.35 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.005 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.012 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.372 Fit side-chains REVERT: A 1 MET cc_start: 0.6121 (tpp) cc_final: 0.5600 (tpp) REVERT: A 3 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: A 16 ARG cc_start: 0.8676 (ttt90) cc_final: 0.8194 (ttm170) REVERT: A 113 LYS cc_start: 0.9306 (mmtm) cc_final: 0.8891 (mttp) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 1.7751 time to fit residues: 92.7072 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.096035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.076536 restraints weight = 4620.481| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 1.58 r_work: 0.2513 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2399 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3432 Z= 0.265 Angle : 0.464 4.273 4659 Z= 0.249 Chirality : 0.043 0.132 505 Planarity : 0.004 0.048 596 Dihedral : 8.535 131.097 475 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.05 % Allowed : 12.28 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.43), residues: 417 helix: 2.00 (0.36), residues: 207 sheet: 0.38 (0.72), residues: 61 loop : -0.41 (0.54), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.006 0.001 HIS A 388 PHE 0.013 0.002 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.403 Fit side-chains REVERT: A 1 MET cc_start: 0.6079 (tpp) cc_final: 0.5621 (tpp) REVERT: A 3 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: A 16 ARG cc_start: 0.8682 (ttt90) cc_final: 0.8204 (ttm170) REVERT: A 113 LYS cc_start: 0.9301 (mmtm) cc_final: 0.8885 (mttp) REVERT: A 312 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8610 (mttp) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 1.6327 time to fit residues: 85.3152 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.0050 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.099969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.080624 restraints weight = 4459.203| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.58 r_work: 0.2642 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3432 Z= 0.157 Angle : 0.429 5.144 4659 Z= 0.230 Chirality : 0.041 0.139 505 Planarity : 0.004 0.049 596 Dihedral : 7.986 121.039 475 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.75 % Allowed : 12.87 % Favored : 85.38 % 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: 1.55 (0.43), residues: 417 helix: 2.22 (0.36), residues: 206 sheet: 0.38 (0.71), residues: 61 loop : -0.36 (0.55), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.398 Fit side-chains REVERT: A 1 MET cc_start: 0.6011 (tpp) cc_final: 0.5566 (tpp) REVERT: A 3 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: A 16 ARG cc_start: 0.8669 (ttt90) cc_final: 0.8188 (ttm170) REVERT: A 312 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8582 (mttp) REVERT: A 388 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8095 (t70) outliers start: 6 outliers final: 1 residues processed: 54 average time/residue: 1.6454 time to fit residues: 91.0313 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 chunk 10 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.100780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.081300 restraints weight = 4483.462| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.60 r_work: 0.2633 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3432 Z= 0.143 Angle : 0.435 6.551 4659 Z= 0.227 Chirality : 0.041 0.134 505 Planarity : 0.004 0.047 596 Dihedral : 7.166 99.619 475 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.17 % Allowed : 14.04 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.43), residues: 417 helix: 2.22 (0.36), residues: 211 sheet: 0.28 (0.72), residues: 60 loop : -0.17 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.003 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.387 Fit side-chains REVERT: A 1 MET cc_start: 0.5899 (tpp) cc_final: 0.5572 (tpp) REVERT: A 3 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: A 16 ARG cc_start: 0.8637 (ttt90) cc_final: 0.8202 (ttm170) REVERT: A 204 LYS cc_start: 0.9221 (ttmt) cc_final: 0.8907 (ttmm) REVERT: A 312 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8551 (mttp) REVERT: A 388 HIS cc_start: 0.8758 (OUTLIER) cc_final: 0.8134 (t70) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 1.5891 time to fit residues: 89.5534 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.098555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.078885 restraints weight = 4451.485| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 1.59 r_work: 0.2617 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3432 Z= 0.217 Angle : 0.469 6.369 4659 Z= 0.247 Chirality : 0.042 0.132 505 Planarity : 0.004 0.047 596 Dihedral : 7.498 105.216 475 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.17 % Allowed : 14.91 % Favored : 83.92 % 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: 1.56 (0.43), residues: 417 helix: 2.11 (0.35), residues: 211 sheet: 0.38 (0.71), residues: 61 loop : -0.23 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.394 Fit side-chains REVERT: A 1 MET cc_start: 0.5868 (tpp) cc_final: 0.5615 (tpp) REVERT: A 3 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: A 16 ARG cc_start: 0.8662 (ttt90) cc_final: 0.8210 (ttm170) REVERT: A 204 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8989 (ttmm) REVERT: A 312 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8606 (mttp) REVERT: A 388 HIS cc_start: 0.8979 (OUTLIER) cc_final: 0.8221 (t70) outliers start: 4 outliers final: 0 residues processed: 55 average time/residue: 1.6469 time to fit residues: 92.7184 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 0.0050 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.081433 restraints weight = 4414.779| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.59 r_work: 0.2577 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3432 Z= 0.170 Angle : 0.449 6.111 4659 Z= 0.236 Chirality : 0.041 0.132 505 Planarity : 0.004 0.047 596 Dihedral : 7.284 101.407 475 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.17 % Allowed : 14.91 % Favored : 83.92 % 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: 1.63 (0.43), residues: 417 helix: 2.18 (0.35), residues: 211 sheet: 0.38 (0.71), residues: 61 loop : -0.20 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.396 Fit side-chains REVERT: A 1 MET cc_start: 0.5816 (tpp) cc_final: 0.5590 (tpp) REVERT: A 3 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: A 16 ARG cc_start: 0.8653 (ttt90) cc_final: 0.8212 (ttm170) REVERT: A 204 LYS cc_start: 0.9226 (ttmt) cc_final: 0.8920 (ttmm) REVERT: A 312 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8573 (mttp) REVERT: A 388 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8222 (t70) outliers start: 4 outliers final: 0 residues processed: 55 average time/residue: 1.6137 time to fit residues: 90.9631 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.081710 restraints weight = 4458.593| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.59 r_work: 0.2647 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3432 Z= 0.181 Angle : 0.457 6.928 4659 Z= 0.240 Chirality : 0.041 0.132 505 Planarity : 0.004 0.047 596 Dihedral : 7.296 101.573 475 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.88 % Allowed : 15.20 % Favored : 83.92 % 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: 1.62 (0.43), residues: 417 helix: 2.18 (0.35), residues: 211 sheet: 0.37 (0.71), residues: 61 loop : -0.21 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2929.16 seconds wall clock time: 50 minutes 33.99 seconds (3033.99 seconds total)