Starting phenix.real_space_refine on Wed Mar 5 20:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6t_28890/03_2025/8f6t_28890.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6t_28890/03_2025/8f6t_28890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6t_28890/03_2025/8f6t_28890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6t_28890/03_2025/8f6t_28890.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6t_28890/03_2025/8f6t_28890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6t_28890/03_2025/8f6t_28890.cif" } resolution = 2.76 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= 0.008 sd= 0.114 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 Fe 3 7.16 5 S 11 5.16 5 C 2261 2.51 5 N 604 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 3473 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3458 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 30, 'TRANS': 397} Chain breaks: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 15 Unusual residues: {' FE': 3, 'D12': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3074 SG CYS A 418 40.499 23.954 46.620 1.00125.12 S ATOM 3095 SG CYS A 421 40.898 27.411 46.825 1.00127.79 S ATOM 3331 SG CYS A 451 38.727 26.710 49.011 1.00124.73 S ATOM 3352 SG CYS A 454 37.613 26.470 45.458 1.00120.95 S Time building chain proxies: 2.75, per 1000 atoms: 0.79 Number of scatterers: 3473 At special positions: 0 Unit cell: (65.268, 81.252, 75.924, 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) Fe 3 26.01 S 11 16.00 O 594 8.00 N 604 7.00 C 2261 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: 0.89 Conformation dependent library (CDL) restraints added in 424.7 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 1 sheets defined 65.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 18 through 25 removed outlier: 3.558A pdb=" N TRP A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 26 through 42 Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 57 through 65 removed outlier: 4.890A pdb=" N TRP A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 4.258A pdb=" N ALA A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 removed outlier: 4.041A pdb=" N VAL A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.672A pdb=" N GLN A 97 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 141 removed outlier: 3.917A pdb=" N HIS A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.595A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 4.004A pdb=" N ASN A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 216 Processing helix chain 'A' and resid 225 through 245 removed outlier: 3.910A pdb=" N MET A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.595A pdb=" N LEU A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.866A pdb=" N SER A 293 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.754A pdb=" N LEU A 325 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.547A pdb=" N VAL A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 363 Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 458 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 424 through 425 165 hydrogen bonds defined for protein. 453 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: 0.90 Time building geometry restraints manager: 1.07 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: 1104 1.34 - 1.46: 717 1.46 - 1.57: 1749 1.57 - 1.69: 0 1.69 - 1.81: 15 Bond restraints: 3585 Sorted by residual: bond pdb=" CA HIS A 314 " pdb=" C HIS A 314 " ideal model delta sigma weight residual 1.523 1.512 0.011 1.30e-02 5.92e+03 7.03e-01 bond pdb=" CG PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.39e-01 bond pdb=" CG1 ILE A 131 " pdb=" CD1 ILE A 131 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.31e-01 bond pdb=" N GLU A 271 " pdb=" CA GLU A 271 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.19e-02 7.06e+03 5.20e-01 bond pdb=" C ILE A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.334 1.350 -0.017 2.34e-02 1.83e+03 5.02e-01 ... (remaining 3580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4637 1.21 - 2.41: 203 2.41 - 3.62: 36 3.62 - 4.82: 15 4.82 - 6.03: 7 Bond angle restraints: 4898 Sorted by residual: angle pdb=" N ASP A 453 " pdb=" CA ASP A 453 " pdb=" C ASP A 453 " ideal model delta sigma weight residual 114.56 110.05 4.51 1.27e+00 6.20e-01 1.26e+01 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" N CYS A 454 " ideal model delta sigma weight residual 119.26 116.45 2.81 1.14e+00 7.69e-01 6.09e+00 angle pdb=" C ASN A 168 " pdb=" N ARG A 169 " pdb=" CA ARG A 169 " ideal model delta sigma weight residual 121.99 118.70 3.29 1.56e+00 4.11e-01 4.46e+00 angle pdb=" CA ASP A 453 " pdb=" C ASP A 453 " pdb=" O ASP A 453 " ideal model delta sigma weight residual 118.55 120.78 -2.23 1.14e+00 7.69e-01 3.83e+00 angle pdb=" N PRO A 374 " pdb=" CA PRO A 374 " pdb=" C PRO A 374 " ideal model delta sigma weight residual 110.70 112.87 -2.17 1.22e+00 6.72e-01 3.17e+00 ... (remaining 4893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 1849 16.14 - 32.29: 184 32.29 - 48.43: 38 48.43 - 64.57: 2 64.57 - 80.71: 1 Dihedral angle restraints: 2074 sinusoidal: 830 harmonic: 1244 Sorted by residual: dihedral pdb=" CA LEU A 367 " pdb=" C LEU A 367 " pdb=" N THR A 368 " pdb=" CA THR A 368 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO A 59 " pdb=" C PRO A 59 " pdb=" N LEU A 60 " pdb=" CA LEU A 60 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TYR A 160 " pdb=" C TYR A 160 " pdb=" N GLY A 161 " pdb=" CA GLY A 161 " ideal model delta harmonic sigma weight residual 180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 267 0.027 - 0.053: 151 0.053 - 0.080: 64 0.080 - 0.107: 27 0.107 - 0.134: 7 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA ARG A 169 " pdb=" N ARG A 169 " pdb=" C ARG A 169 " pdb=" CB ARG A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL A 347 " pdb=" N VAL A 347 " pdb=" C VAL A 347 " pdb=" CB VAL A 347 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE A 445 " pdb=" N ILE A 445 " pdb=" C ILE A 445 " pdb=" CB ILE A 445 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 513 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 373 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 374 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 180 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.08e+00 pdb=" N PRO A 181 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 440 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 441 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.019 5.00e-02 4.00e+02 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 52 2.68 - 3.23: 3346 3.23 - 3.79: 5315 3.79 - 4.34: 7139 4.34 - 4.90: 11788 Nonbonded interactions: 27640 Sorted by model distance: nonbonded pdb=" NE2 HIS A 167 " pdb="FE FE A 502 " model vdw 2.119 2.340 nonbonded pdb=" NE2 HIS A 272 " pdb="FE FE A 501 " model vdw 2.163 2.340 nonbonded pdb=" NE2 HIS A 314 " pdb="FE FE A 502 " model vdw 2.167 2.340 nonbonded pdb=" NE2 HIS A 141 " pdb="FE FE A 502 " model vdw 2.198 2.340 nonbonded pdb=" ND2 ASN A 129 " pdb=" OE1 GLN A 256 " model vdw 2.215 3.120 ... (remaining 27635 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: 0.200 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.004 0.029 3585 Z= 0.285 Angle : 0.629 6.030 4898 Z= 0.344 Chirality : 0.041 0.134 516 Planarity : 0.005 0.049 624 Dihedral : 12.871 80.711 1278 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.80 (0.42), residues: 424 helix: 1.16 (0.36), residues: 239 sheet: None (None), residues: 0 loop : -0.22 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.007 0.001 HIS A 315 PHE 0.010 0.001 PHE A 26 TYR 0.010 0.001 TYR A 423 ARG 0.004 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.0752 time to fit residues: 33.6982 Evaluate side-chains 21 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.064683 restraints weight = 7117.122| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.65 r_work: 0.2698 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3585 Z= 0.176 Angle : 0.559 7.031 4898 Z= 0.282 Chirality : 0.039 0.113 516 Planarity : 0.005 0.046 624 Dihedral : 5.352 49.317 485 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.68 % Allowed : 5.31 % Favored : 93.02 % 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: 1.20 (0.43), residues: 424 helix: 1.43 (0.37), residues: 239 sheet: None (None), residues: 0 loop : 0.06 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 442 HIS 0.008 0.001 HIS A 315 PHE 0.010 0.001 PHE A 193 TYR 0.009 0.001 TYR A 160 ARG 0.002 0.000 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.367 Fit side-chains REVERT: A 226 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: A 271 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8013 (mt-10) outliers start: 6 outliers final: 2 residues processed: 28 average time/residue: 0.8388 time to fit residues: 24.8209 Evaluate side-chains 26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.064143 restraints weight = 6974.704| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.61 r_work: 0.2686 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3585 Z= 0.191 Angle : 0.544 5.653 4898 Z= 0.275 Chirality : 0.039 0.143 516 Planarity : 0.005 0.046 624 Dihedral : 5.285 53.133 485 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 9.22 % Favored : 89.39 % 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: 1.10 (0.43), residues: 424 helix: 1.31 (0.36), residues: 243 sheet: None (None), residues: 0 loop : 0.05 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 442 HIS 0.005 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.008 0.001 TYR A 85 ARG 0.001 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.356 Fit side-chains REVERT: A 42 ASP cc_start: 0.8810 (t0) cc_final: 0.8542 (t0) REVERT: A 226 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: A 271 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8057 (mt-10) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 1.0343 time to fit residues: 27.1649 Evaluate side-chains 26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.064683 restraints weight = 7059.586| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.63 r_work: 0.2699 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3585 Z= 0.173 Angle : 0.520 5.585 4898 Z= 0.263 Chirality : 0.038 0.120 516 Planarity : 0.005 0.046 624 Dihedral : 5.225 55.492 485 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.40 % Allowed : 8.94 % Favored : 89.66 % 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: 1.14 (0.43), residues: 424 helix: 1.33 (0.36), residues: 243 sheet: None (None), residues: 0 loop : 0.10 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.005 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.007 0.001 TYR A 85 ARG 0.003 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.429 Fit side-chains REVERT: A 42 ASP cc_start: 0.8798 (t0) cc_final: 0.8544 (t0) REVERT: A 63 TRP cc_start: 0.9065 (t60) cc_final: 0.8590 (t60) REVERT: A 226 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8290 (mp0) outliers start: 5 outliers final: 2 residues processed: 25 average time/residue: 0.9536 time to fit residues: 25.2169 Evaluate side-chains 26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.079409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.064674 restraints weight = 7167.663| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.68 r_work: 0.2697 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3585 Z= 0.178 Angle : 0.522 5.594 4898 Z= 0.263 Chirality : 0.038 0.121 516 Planarity : 0.005 0.045 624 Dihedral : 5.108 54.731 485 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 10.06 % Favored : 88.55 % 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: 1.17 (0.43), residues: 424 helix: 1.32 (0.36), residues: 243 sheet: None (None), residues: 0 loop : 0.16 (0.48), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.004 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.007 0.001 TYR A 85 ARG 0.004 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.392 Fit side-chains REVERT: A 42 ASP cc_start: 0.8816 (t0) cc_final: 0.8522 (t0) REVERT: A 63 TRP cc_start: 0.9051 (t60) cc_final: 0.8575 (t60) REVERT: A 226 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8313 (mp0) outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.9241 time to fit residues: 25.3615 Evaluate side-chains 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.065108 restraints weight = 7206.556| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.65 r_work: 0.2704 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3585 Z= 0.176 Angle : 0.512 5.590 4898 Z= 0.259 Chirality : 0.038 0.121 516 Planarity : 0.005 0.045 624 Dihedral : 5.023 53.298 485 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.96 % Allowed : 10.34 % Favored : 87.71 % 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: 1.22 (0.43), residues: 424 helix: 1.38 (0.37), residues: 241 sheet: None (None), residues: 0 loop : 0.15 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.005 0.001 HIS A 315 PHE 0.008 0.001 PHE A 193 TYR 0.007 0.001 TYR A 85 ARG 0.005 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.360 Fit side-chains REVERT: A 42 ASP cc_start: 0.8832 (t0) cc_final: 0.8526 (t0) REVERT: A 63 TRP cc_start: 0.9018 (t60) cc_final: 0.8568 (t60) REVERT: A 226 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8304 (mp0) outliers start: 7 outliers final: 2 residues processed: 30 average time/residue: 0.8966 time to fit residues: 28.3138 Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067349 restraints weight = 7053.645| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.66 r_work: 0.2751 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3585 Z= 0.160 Angle : 0.508 6.227 4898 Z= 0.255 Chirality : 0.037 0.122 516 Planarity : 0.004 0.044 624 Dihedral : 4.807 48.632 485 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.68 % Allowed : 10.34 % Favored : 87.99 % 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: 1.23 (0.44), residues: 424 helix: 1.36 (0.37), residues: 241 sheet: None (None), residues: 0 loop : 0.21 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.003 0.000 HIS A 311 PHE 0.010 0.001 PHE A 193 TYR 0.007 0.001 TYR A 85 ARG 0.002 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.303 Fit side-chains REVERT: A 42 ASP cc_start: 0.8834 (t0) cc_final: 0.8533 (t0) REVERT: A 63 TRP cc_start: 0.8996 (t60) cc_final: 0.8507 (t60) REVERT: A 226 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: A 271 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7793 (tt0) outliers start: 6 outliers final: 2 residues processed: 27 average time/residue: 0.9414 time to fit residues: 26.7129 Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 271 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.0020 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.0010 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.067131 restraints weight = 7048.890| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.67 r_work: 0.2745 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3585 Z= 0.164 Angle : 0.514 5.568 4898 Z= 0.259 Chirality : 0.037 0.123 516 Planarity : 0.004 0.044 624 Dihedral : 4.618 44.301 485 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.40 % Allowed : 11.45 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.43), residues: 424 helix: 1.38 (0.37), residues: 241 sheet: None (None), residues: 0 loop : 0.27 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.003 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.006 0.001 TYR A 85 ARG 0.003 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.357 Fit side-chains REVERT: A 42 ASP cc_start: 0.8838 (t0) cc_final: 0.8543 (t0) REVERT: A 63 TRP cc_start: 0.8993 (t60) cc_final: 0.8504 (t60) REVERT: A 142 LYS cc_start: 0.8436 (mptt) cc_final: 0.8038 (mmtp) REVERT: A 226 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: A 271 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7764 (tt0) outliers start: 5 outliers final: 1 residues processed: 29 average time/residue: 0.9679 time to fit residues: 29.4319 Evaluate side-chains 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 271 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 0.0970 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067510 restraints weight = 6941.131| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.65 r_work: 0.2759 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3585 Z= 0.163 Angle : 0.506 5.649 4898 Z= 0.254 Chirality : 0.037 0.122 516 Planarity : 0.004 0.044 624 Dihedral : 4.508 39.625 485 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.12 % Allowed : 12.29 % Favored : 86.59 % 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: 1.30 (0.44), residues: 424 helix: 1.39 (0.37), residues: 241 sheet: None (None), residues: 0 loop : 0.29 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.002 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.006 0.001 TYR A 85 ARG 0.002 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.356 Fit side-chains REVERT: A 42 ASP cc_start: 0.8859 (t0) cc_final: 0.8533 (t0) REVERT: A 63 TRP cc_start: 0.8978 (t60) cc_final: 0.8485 (t60) REVERT: A 142 LYS cc_start: 0.8403 (mptt) cc_final: 0.8011 (mmtp) REVERT: A 226 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: A 271 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7744 (tt0) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.9884 time to fit residues: 27.9872 Evaluate side-chains 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 367 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.067502 restraints weight = 7058.031| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.69 r_work: 0.2751 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3585 Z= 0.166 Angle : 0.515 6.080 4898 Z= 0.259 Chirality : 0.037 0.122 516 Planarity : 0.004 0.044 624 Dihedral : 4.476 36.695 485 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.12 % Allowed : 12.29 % Favored : 86.59 % 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: 1.32 (0.44), residues: 424 helix: 1.39 (0.37), residues: 241 sheet: None (None), residues: 0 loop : 0.32 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.003 0.001 HIS A 315 PHE 0.010 0.001 PHE A 193 TYR 0.006 0.001 TYR A 259 ARG 0.003 0.000 ARG A 433 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.409 Fit side-chains REVERT: A 42 ASP cc_start: 0.8867 (t0) cc_final: 0.8540 (t0) REVERT: A 63 TRP cc_start: 0.8990 (t60) cc_final: 0.8492 (t60) REVERT: A 142 LYS cc_start: 0.8428 (mptt) cc_final: 0.8029 (mmtp) REVERT: A 226 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: A 271 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7789 (tt0) outliers start: 4 outliers final: 1 residues processed: 26 average time/residue: 1.0598 time to fit residues: 28.8551 Evaluate side-chains 26 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 271 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.065791 restraints weight = 7142.291| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.70 r_work: 0.2721 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3585 Z= 0.188 Angle : 0.523 5.931 4898 Z= 0.264 Chirality : 0.038 0.121 516 Planarity : 0.004 0.044 624 Dihedral : 4.645 40.088 485 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.84 % Allowed : 12.57 % Favored : 86.59 % 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: 1.32 (0.43), residues: 424 helix: 1.54 (0.37), residues: 235 sheet: None (None), residues: 0 loop : 0.13 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 21 HIS 0.004 0.001 HIS A 315 PHE 0.009 0.001 PHE A 193 TYR 0.007 0.001 TYR A 93 ARG 0.002 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.79 seconds wall clock time: 37 minutes 6.41 seconds (2226.41 seconds total)