Starting phenix.real_space_refine on Wed Mar 5 21:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcs_38253/03_2025/8xcs_38253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcs_38253/03_2025/8xcs_38253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcs_38253/03_2025/8xcs_38253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcs_38253/03_2025/8xcs_38253.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcs_38253/03_2025/8xcs_38253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcs_38253/03_2025/8xcs_38253.cif" } resolution = 2.63 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 14 5.16 5 C 2121 2.51 5 N 567 2.21 5 O 655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3360 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3281 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 79 Unusual residues: {'AKG': 1, 'NDP': 1, 'NH4': 1} Classifications: {'undetermined': 3, 'water': 20} Link IDs: {None: 22} Time building chain proxies: 2.87, per 1000 atoms: 0.85 Number of scatterers: 3360 At special positions: 0 Unit cell: (71.44, 69.184, 68.432, 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 14 16.00 P 3 15.00 O 655 8.00 N 567 7.00 C 2121 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: 0.93 Conformation dependent library (CDL) restraints added in 439.1 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 55.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 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: 3.815A 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: 3.919A 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: 4.472A 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: 6.831A 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: 6.471A 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: 1.38 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: 1004 1.34 - 1.45: 483 1.45 - 1.57: 1899 1.57 - 1.69: 2 1.69 - 1.81: 27 Bond restraints: 3415 Sorted by residual: bond pdb=" O1N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.477 1.550 -0.073 1.00e-02 1.00e+04 5.28e+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 4.94e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.559 0.198 3.50e-02 8.16e+02 3.22e+01 bond pdb=" C1 AKG A 502 " pdb=" C2 AKG A 502 " ideal model delta sigma weight residual 1.559 1.461 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C6A NDP A 501 " pdb=" N1A NDP A 501 " ideal model delta sigma weight residual 1.368 1.253 0.115 2.90e-02 1.19e+03 1.58e+01 ... (remaining 3410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 4600 4.42 - 8.85: 23 8.85 - 13.27: 10 13.27 - 17.69: 4 17.69 - 22.12: 1 Bond angle restraints: 4638 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 105.41 127.53 -22.12 2.71e+00 1.37e-01 6.68e+01 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 119.24 -15.40 1.91e+00 2.73e-01 6.47e+01 angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 122.52 -14.78 1.95e+00 2.62e-01 5.72e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 109.42 8.04 1.17e+00 7.36e-01 4.75e+01 angle pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.33 108.86 8.47 1.48e+00 4.57e-01 3.28e+01 ... (remaining 4633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 1931 30.95 - 61.89: 84 61.89 - 92.84: 7 92.84 - 123.78: 0 123.78 - 154.73: 1 Dihedral angle restraints: 2023 sinusoidal: 828 harmonic: 1195 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 20.31 154.73 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 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB LYS A 304 " pdb=" CG LYS A 304 " pdb=" CD LYS A 304 " pdb=" CE LYS A 304 " ideal model delta sinusoidal sigma weight residual 180.00 121.19 58.81 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 443 0.079 - 0.159: 52 0.159 - 0.238: 3 0.238 - 0.318: 3 0.318 - 0.397: 3 Chirality restraints: 504 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 3.95e+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 3.42e+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 3.16e+00 ... (remaining 501 not shown) Planarity restraints: 592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 501 " -0.139 2.00e-02 2.50e+03 8.17e-02 8.34e+01 pdb=" C3N NDP A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C4N NDP A 501 " -0.026 2.00e-02 2.50e+03 pdb=" C7N NDP A 501 " 0.058 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.035 2.00e-02 2.50e+03 6.15e-02 3.78e+01 pdb=" C5N NDP A 501 " 0.078 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 394 " 0.021 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C HIS A 394 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS A 394 " 0.026 2.00e-02 2.50e+03 pdb=" N MET A 395 " 0.024 2.00e-02 2.50e+03 ... (remaining 589 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1265 2.88 - 3.39: 3295 3.39 - 3.89: 6079 3.89 - 4.40: 7212 4.40 - 4.90: 11655 Nonbonded interactions: 29506 Sorted by model distance: nonbonded pdb=" O HIS A 61 " pdb=" O HOH A 601 " model vdw 2.381 3.040 nonbonded pdb=" O ASP A 145 " pdb=" O HOH A 602 " model vdw 2.445 3.040 nonbonded pdb=" O VAL A 317 " pdb=" ND2 ASN A 344 " model vdw 2.448 3.120 nonbonded pdb=" O ARG A 65 " pdb=" O HOH A 603 " model vdw 2.461 3.040 nonbonded pdb=" O THR A 148 " pdb=" O HOH A 602 " model vdw 2.469 3.040 ... (remaining 29501 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: 1.230 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: 15.400 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:14.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 3415 Z= 0.517 Angle : 1.096 22.116 4638 Z= 0.584 Chirality : 0.059 0.397 504 Planarity : 0.006 0.082 592 Dihedral : 16.414 154.727 1261 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.69 % Allowed : 3.52 % Favored : 91.79 % 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: 0.58 (0.43), residues: 416 helix: 0.93 (0.36), residues: 210 sheet: 0.54 (0.74), residues: 60 loop : -0.33 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.478 Fit side-chains REVERT: A 12 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (mptt) outliers start: 16 outliers final: 2 residues processed: 76 average time/residue: 1.6137 time to fit residues: 125.3674 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 19 GLN 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: 5.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.079925 restraints weight = 4250.924| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 1.52 r_work: 0.2657 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3415 Z= 0.247 Angle : 0.523 5.391 4638 Z= 0.278 Chirality : 0.044 0.136 504 Planarity : 0.005 0.043 592 Dihedral : 10.738 154.483 477 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.23 % Allowed : 10.85 % Favored : 85.92 % 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: 1.29 (0.44), residues: 416 helix: 1.77 (0.36), residues: 211 sheet: 0.38 (0.72), residues: 61 loop : -0.24 (0.57), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 364 HIS 0.006 0.002 HIS A 388 PHE 0.015 0.002 PHE A 341 TYR 0.013 0.002 TYR A 363 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.391 Fit side-chains REVERT: A 16 ARG cc_start: 0.8518 (ttm170) cc_final: 0.8260 (ttm170) REVERT: A 113 LYS cc_start: 0.8990 (mttp) cc_final: 0.8502 (mtpt) REVERT: A 229 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8631 (tttp) REVERT: A 371 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7659 (pt0) outliers start: 11 outliers final: 1 residues processed: 53 average time/residue: 1.6770 time to fit residues: 91.0337 Evaluate side-chains 44 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 371 GLU 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 1 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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 = 0.3178 r_free = 0.3178 target = 0.106378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.080480 restraints weight = 4170.731| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.49 r_work: 0.2686 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3415 Z= 0.198 Angle : 0.479 4.390 4638 Z= 0.252 Chirality : 0.042 0.133 504 Planarity : 0.004 0.044 592 Dihedral : 9.120 141.928 470 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 12.61 % Favored : 85.34 % 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 (0.44), residues: 416 helix: 2.04 (0.36), residues: 211 sheet: 0.38 (0.72), residues: 61 loop : -0.12 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 364 HIS 0.005 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.421 Fit side-chains REVERT: A 371 GLU cc_start: 0.8047 (pt0) cc_final: 0.7709 (pt0) outliers start: 7 outliers final: 1 residues processed: 47 average time/residue: 1.6316 time to fit residues: 78.7138 Evaluate side-chains 41 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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 = 0.3170 r_free = 0.3170 target = 0.105896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.079962 restraints weight = 4276.148| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.52 r_work: 0.2672 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3415 Z= 0.195 Angle : 0.469 4.949 4638 Z= 0.248 Chirality : 0.042 0.131 504 Planarity : 0.004 0.044 592 Dihedral : 8.571 124.382 470 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.52 % Allowed : 11.14 % Favored : 85.34 % 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 (0.44), residues: 416 helix: 2.11 (0.35), residues: 211 sheet: 0.42 (0.73), residues: 61 loop : -0.13 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.005 0.001 HIS A 388 PHE 0.014 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.392 Fit side-chains REVERT: A 4 ILE cc_start: 0.8181 (tp) cc_final: 0.7898 (tt) REVERT: A 19 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: A 246 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7647 (mtt180) REVERT: A 371 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: A 388 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.7821 (t70) outliers start: 12 outliers final: 2 residues processed: 51 average time/residue: 1.5667 time to fit residues: 81.9105 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU 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 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 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 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.079767 restraints weight = 4257.931| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.51 r_work: 0.2670 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3415 Z= 0.199 Angle : 0.470 4.672 4638 Z= 0.249 Chirality : 0.043 0.135 504 Planarity : 0.004 0.045 592 Dihedral : 8.187 110.088 470 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.35 % Allowed : 13.20 % Favored : 84.46 % 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 (0.44), residues: 416 helix: 2.15 (0.36), residues: 211 sheet: 0.41 (0.73), residues: 61 loop : -0.16 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.005 0.001 HIS A 388 PHE 0.014 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.356 Fit side-chains REVERT: A 4 ILE cc_start: 0.8189 (tp) cc_final: 0.7884 (tt) REVERT: A 19 GLN cc_start: 0.8149 (pt0) cc_final: 0.7868 (pt0) REVERT: A 246 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7636 (mtt180) REVERT: A 371 GLU cc_start: 0.8056 (pt0) cc_final: 0.7739 (pt0) REVERT: A 388 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.7903 (t70) outliers start: 8 outliers final: 1 residues processed: 49 average time/residue: 1.6261 time to fit residues: 81.5885 Evaluate side-chains 45 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG 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 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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 = 0.3195 r_free = 0.3195 target = 0.107562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.082053 restraints weight = 4448.839| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 1.50 r_work: 0.2666 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3415 Z= 0.155 Angle : 0.448 4.509 4638 Z= 0.236 Chirality : 0.042 0.133 504 Planarity : 0.004 0.045 592 Dihedral : 7.418 97.388 470 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.93 % Allowed : 12.02 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.44), residues: 416 helix: 2.24 (0.36), residues: 211 sheet: 0.36 (0.72), residues: 61 loop : -0.09 (0.59), residues: 144 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 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.840 Fit side-chains REVERT: A 4 ILE cc_start: 0.8090 (tp) cc_final: 0.7784 (tt) REVERT: A 246 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7498 (mtt180) REVERT: A 371 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: A 388 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8087 (t70) outliers start: 10 outliers final: 2 residues processed: 51 average time/residue: 1.7511 time to fit residues: 92.3876 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU 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 16 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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 = 0.3138 r_free = 0.3138 target = 0.103417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.078060 restraints weight = 4300.027| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.42 r_work: 0.2661 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3415 Z= 0.304 Angle : 0.530 4.881 4638 Z= 0.281 Chirality : 0.045 0.139 504 Planarity : 0.005 0.046 592 Dihedral : 7.704 99.015 470 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.35 % Allowed : 13.49 % Favored : 84.16 % 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 (0.44), residues: 416 helix: 2.19 (0.35), residues: 206 sheet: 0.34 (0.72), residues: 61 loop : -0.35 (0.57), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 30 HIS 0.007 0.002 HIS A 388 PHE 0.020 0.002 PHE A 341 TYR 0.015 0.002 TYR A 363 ARG 0.001 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.410 Fit side-chains REVERT: A 4 ILE cc_start: 0.8275 (tp) cc_final: 0.7956 (tt) REVERT: A 246 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7585 (mtt180) REVERT: A 371 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7868 (pt0) outliers start: 8 outliers final: 2 residues processed: 44 average time/residue: 1.7408 time to fit residues: 78.4430 Evaluate side-chains 44 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU 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 40 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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 = 0.3204 r_free = 0.3204 target = 0.108062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.082705 restraints weight = 4377.179| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.48 r_work: 0.2692 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3415 Z= 0.139 Angle : 0.453 4.291 4638 Z= 0.237 Chirality : 0.041 0.131 504 Planarity : 0.004 0.047 592 Dihedral : 7.150 95.749 470 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.64 % Allowed : 12.90 % Favored : 84.46 % 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: 1.73 (0.44), residues: 416 helix: 2.25 (0.36), residues: 211 sheet: 0.33 (0.72), residues: 61 loop : -0.12 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.418 Fit side-chains REVERT: A 4 ILE cc_start: 0.8096 (tp) cc_final: 0.7780 (tt) REVERT: A 78 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: A 246 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7454 (mtt180) REVERT: A 371 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7727 (pt0) REVERT: A 388 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8258 (t70) outliers start: 9 outliers final: 1 residues processed: 48 average time/residue: 1.6609 time to fit residues: 81.6745 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU 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 8 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.0570 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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 = 0.3220 r_free = 0.3220 target = 0.109226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.083865 restraints weight = 4358.824| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.49 r_work: 0.2721 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3415 Z= 0.137 Angle : 0.456 4.643 4638 Z= 0.238 Chirality : 0.041 0.125 504 Planarity : 0.004 0.045 592 Dihedral : 6.953 92.942 470 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.64 % Allowed : 13.20 % Favored : 84.16 % 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: 1.84 (0.44), residues: 416 helix: 2.34 (0.36), residues: 211 sheet: 0.43 (0.73), residues: 61 loop : -0.07 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.002 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.401 Fit side-chains REVERT: A 4 ILE cc_start: 0.8047 (tp) cc_final: 0.7720 (tt) REVERT: A 246 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7476 (mtt180) REVERT: A 368 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7444 (mt-10) REVERT: A 371 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7744 (pt0) REVERT: A 388 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8290 (t70) outliers start: 9 outliers final: 1 residues processed: 51 average time/residue: 1.6623 time to fit residues: 86.8159 Evaluate side-chains 51 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 371 GLU 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 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 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 = 0.3187 r_free = 0.3187 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.081437 restraints weight = 4377.667| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.48 r_work: 0.2677 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3415 Z= 0.173 Angle : 0.478 5.522 4638 Z= 0.250 Chirality : 0.042 0.130 504 Planarity : 0.004 0.046 592 Dihedral : 7.100 92.754 470 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.47 % Allowed : 14.37 % Favored : 84.16 % 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: 1.79 (0.44), residues: 416 helix: 2.31 (0.35), residues: 211 sheet: 0.41 (0.73), residues: 61 loop : -0.09 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.010 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.403 Fit side-chains REVERT: A 4 ILE cc_start: 0.8072 (tp) cc_final: 0.7747 (tt) REVERT: A 371 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: A 388 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8173 (t70) outliers start: 5 outliers final: 1 residues processed: 45 average time/residue: 1.7936 time to fit residues: 82.6597 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 371 GLU 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 3 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.109292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.083959 restraints weight = 4356.529| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.48 r_work: 0.2733 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3415 Z= 0.136 Angle : 0.455 5.417 4638 Z= 0.237 Chirality : 0.041 0.130 504 Planarity : 0.004 0.046 592 Dihedral : 6.910 90.655 470 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.76 % Allowed : 13.49 % Favored : 84.75 % 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: 1.82 (0.44), residues: 416 helix: 2.32 (0.36), residues: 211 sheet: 0.44 (0.73), residues: 61 loop : -0.08 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.007 0.001 TYR A 363 ARG 0.001 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.37 seconds wall clock time: 49 minutes 42.82 seconds (2982.82 seconds total)