Starting phenix.real_space_refine on Mon Jan 13 19:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xd6_38267/01_2025/8xd6_38267_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xd6_38267/01_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_38267/01_2025/8xd6_38267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xd6_38267/01_2025/8xd6_38267.map" model { file = "/net/cci-nas-00/data/ceres_data/8xd6_38267/01_2025/8xd6_38267_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xd6_38267/01_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-5571/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: 2.96, per 1000 atoms: 0.87 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: 0.91 Conformation dependent library (CDL) restraints added in 428.4 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: 0.47 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: 1.08 Time building geometry restraints manager: 1.05 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- 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 : 0.381 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 1.5882 time to fit residues: 112.1459 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 : 0.538 ------------------------------------------------------------------------------- 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 = 0.085791 restraints weight = 4398.787| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 1.51 r_work: 0.2579 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 3.27 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 : 0.384 Fit side-chains REVERT: A 1 MET cc_start: 0.6207 (tpp) cc_final: 0.5634 (tpp) REVERT: A 16 ARG cc_start: 0.8787 (ttt90) cc_final: 0.8251 (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: 1.7506 time to fit residues: 103.9468 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 : 0.412 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.3100 r_free = 0.3100 target = 0.104511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.087195 restraints weight = 4363.070| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 1.47 r_work: 0.2608 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3432 Z= 0.206 Angle : 0.463 4.203 4659 Z= 0.245 Chirality : 0.042 0.134 505 Planarity : 0.004 0.042 596 Dihedral : 9.650 147.516 478 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.05 % Allowed : 11.40 % Favored : 86.55 % 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: 1.98 (0.36), residues: 212 sheet: 0.52 (0.73), residues: 61 loop : -0.11 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.004 0.002 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.011 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 : 0.379 Fit side-chains REVERT: A 1 MET cc_start: 0.6142 (tpp) cc_final: 0.5575 (tpp) REVERT: A 16 ARG cc_start: 0.8757 (ttt90) cc_final: 0.8360 (ttm170) REVERT: A 113 LYS cc_start: 0.9302 (mmtm) cc_final: 0.8928 (mttp) REVERT: A 118 ARG cc_start: 0.8688 (mmp80) cc_final: 0.8484 (mmp80) outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 1.7815 time to fit residues: 96.6571 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.099852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.080454 restraints weight = 4471.415| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 1.58 r_work: 0.2584 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3432 Z= 0.175 Angle : 0.433 3.993 4659 Z= 0.230 Chirality : 0.042 0.133 505 Planarity : 0.004 0.043 596 Dihedral : 8.560 137.621 475 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.46 % Allowed : 12.28 % Favored : 86.26 % 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: 1.64 (0.43), residues: 417 helix: 2.05 (0.36), residues: 212 sheet: 0.52 (0.72), residues: 61 loop : -0.04 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.003 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: 5 poor density : 52 time to evaluate : 0.406 Fit side-chains REVERT: A 1 MET cc_start: 0.6033 (tpp) cc_final: 0.5543 (tpp) REVERT: A 16 ARG cc_start: 0.8719 (ttt90) cc_final: 0.8216 (ttm170) REVERT: A 25 GLU cc_start: 0.8424 (tp30) cc_final: 0.8213 (mm-30) REVERT: A 118 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8335 (mmp80) REVERT: A 149 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8104 (p0) REVERT: A 312 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: A 388 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8124 (t70) outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 1.7107 time to fit residues: 94.6158 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 : 0.465 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.098861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.079249 restraints weight = 4516.631| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.59 r_work: 0.2630 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3432 Z= 0.177 Angle : 0.427 4.051 4659 Z= 0.228 Chirality : 0.042 0.131 505 Planarity : 0.004 0.043 596 Dihedral : 8.189 128.066 475 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: 1.66 (0.43), residues: 417 helix: 2.09 (0.35), residues: 212 sheet: 0.49 (0.72), residues: 61 loop : -0.06 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.010 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 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.400 Fit side-chains REVERT: A 1 MET cc_start: 0.5983 (tpp) cc_final: 0.5539 (tpp) REVERT: A 3 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: A 16 ARG cc_start: 0.8674 (ttt90) cc_final: 0.8216 (ttm170) REVERT: A 149 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8092 (p0) REVERT: A 388 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8070 (t70) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 1.6927 time to fit residues: 91.8364 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 : 0.396 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 149 ASN A 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.096959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.077369 restraints weight = 4597.235| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 1.59 r_work: 0.2523 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3432 Z= 0.288 Angle : 0.484 5.048 4659 Z= 0.257 Chirality : 0.044 0.131 505 Planarity : 0.004 0.044 596 Dihedral : 8.169 121.267 475 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.75 % Allowed : 13.45 % 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: 1.50 (0.43), residues: 417 helix: 2.10 (0.36), residues: 207 sheet: 0.40 (0.71), residues: 61 loop : -0.28 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.006 0.001 HIS A 388 PHE 0.016 0.002 PHE A 341 TYR 0.014 0.001 TYR A 363 ARG 0.001 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 55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.372 Fit side-chains REVERT: A 1 MET cc_start: 0.6098 (tpp) cc_final: 0.5648 (tpp) REVERT: A 3 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: A 16 ARG cc_start: 0.8695 (ttt90) cc_final: 0.8227 (ttm170) REVERT: A 113 LYS cc_start: 0.9305 (mmtm) cc_final: 0.8890 (mttp) REVERT: A 312 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8596 (mttp) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 1.7004 time to fit residues: 88.7650 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 : 0.314 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.2971 r_free = 0.2971 target = 0.097366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.077774 restraints weight = 4497.202| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 1.58 r_work: 0.2610 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3432 Z= 0.218 Angle : 0.454 4.758 4659 Z= 0.241 Chirality : 0.042 0.133 505 Planarity : 0.004 0.047 596 Dihedral : 7.868 114.811 475 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.75 % Allowed : 13.45 % 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: 1.52 (0.43), residues: 417 helix: 2.13 (0.36), residues: 207 sheet: 0.35 (0.71), residues: 61 loop : -0.28 (0.55), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.005 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.011 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 55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.401 Fit side-chains REVERT: A 1 MET cc_start: 0.6028 (tpp) cc_final: 0.5665 (tpp) REVERT: A 3 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: A 16 ARG cc_start: 0.8677 (ttt90) cc_final: 0.8210 (ttm170) REVERT: A 312 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8605 (mttp) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 1.7412 time to fit residues: 90.9092 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 : 0.422 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3035 r_free = 0.3035 target = 0.101202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.082030 restraints weight = 4476.609| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 1.57 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: 0.8970 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3432 Z= 0.181 Angle : 0.444 5.643 4659 Z= 0.236 Chirality : 0.042 0.132 505 Planarity : 0.004 0.047 596 Dihedral : 7.550 106.869 475 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.75 % Allowed : 13.16 % Favored : 85.09 % 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: 2.07 (0.36), residues: 212 sheet: 0.33 (0.71), residues: 61 loop : -0.14 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.004 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 *********************** 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 55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.380 Fit side-chains REVERT: A 1 MET cc_start: 0.5889 (tpp) cc_final: 0.5538 (tpp) REVERT: A 3 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: A 16 ARG cc_start: 0.8641 (ttt90) cc_final: 0.8180 (ttm170) REVERT: A 312 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: A 388 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8135 (t70) outliers start: 6 outliers final: 1 residues processed: 51 average time/residue: 1.6958 time to fit residues: 88.5818 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 : 0.397 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.0370 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.104165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.084944 restraints weight = 4397.199| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.58 r_work: 0.2681 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3432 Z= 0.145 Angle : 0.427 5.797 4659 Z= 0.226 Chirality : 0.041 0.132 505 Planarity : 0.004 0.047 596 Dihedral : 7.132 99.393 475 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.17 % Allowed : 13.45 % 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: 1.69 (0.43), residues: 417 helix: 2.22 (0.35), residues: 211 sheet: 0.25 (0.71), residues: 62 loop : -0.08 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.000 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.002 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 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.418 Fit side-chains REVERT: A 1 MET cc_start: 0.5853 (tpp) cc_final: 0.5570 (tpp) REVERT: A 3 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: A 16 ARG cc_start: 0.8643 (ttt90) cc_final: 0.8206 (ttm170) REVERT: A 204 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8904 (ttmm) REVERT: A 312 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8560 (mttp) REVERT: A 388 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8011 (t70) outliers start: 4 outliers final: 1 residues processed: 56 average time/residue: 1.6510 time to fit residues: 94.6749 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 : 0.375 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.101414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.081924 restraints weight = 4422.820| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.60 r_work: 0.2612 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1792 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= 0.173 Angle : 0.461 7.018 4659 Z= 0.240 Chirality : 0.041 0.131 505 Planarity : 0.004 0.046 596 Dihedral : 7.175 100.248 475 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.88 % Allowed : 14.62 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.43), residues: 417 helix: 2.24 (0.36), residues: 211 sheet: 0.40 (0.71), residues: 61 loop : -0.15 (0.56), residues: 145 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 0.009 0.001 PHE A 341 TYR 0.008 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 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.394 Fit side-chains REVERT: A 1 MET cc_start: 0.5793 (tpp) cc_final: 0.5577 (tpp) REVERT: A 16 ARG cc_start: 0.8640 (ttt90) cc_final: 0.8206 (ttm170) REVERT: A 149 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.7940 (p0) REVERT: A 204 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8918 (ttmm) REVERT: A 388 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8166 (t70) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 1.6948 time to fit residues: 88.5559 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 : 0.390 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 = 0.3007 r_free = 0.3007 target = 0.099816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.080186 restraints weight = 4483.922| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.60 r_work: 0.2595 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3432 Z= 0.199 Angle : 0.460 6.123 4659 Z= 0.241 Chirality : 0.042 0.132 505 Planarity : 0.004 0.046 596 Dihedral : 7.324 101.922 475 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.17 % Allowed : 14.33 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.43), residues: 417 helix: 2.20 (0.36), residues: 211 sheet: 0.36 (0.71), residues: 61 loop : -0.19 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2902.30 seconds wall clock time: 52 minutes 19.99 seconds (3139.99 seconds total)