Starting phenix.real_space_refine on Tue Feb 11 01:21:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6t_28890/02_2025/8f6t_28890.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6t_28890/02_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_28890/02_2025/8f6t_28890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6t_28890/02_2025/8f6t_28890.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6t_28890/02_2025/8f6t_28890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6t_28890/02_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-5592/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: 2.63, per 1000 atoms: 0.76 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: 0.87 Conformation dependent library (CDL) restraints added in 412.7 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: 0.89 Time building geometry restraints manager: 0.91 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: 0.100 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: 0.030 Set scattering table: 0.040 Process input model: 12.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- 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 : 0.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 1.0999 time to fit residues: 34.4476 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 : 0.359 ------------------------------------------------------------------------------- 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 : 0.315 Fit side-chains REVERT: A 226 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: A 271 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8013 (mt-10) outliers start: 6 outliers final: 2 residues processed: 28 average time/residue: 0.8417 time to fit residues: 24.8482 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 : 0.367 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.077171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.062289 restraints weight = 7020.549| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.62 r_work: 0.2654 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3585 Z= 0.248 Angle : 0.570 6.263 4898 Z= 0.289 Chirality : 0.040 0.131 516 Planarity : 0.005 0.047 624 Dihedral : 5.483 57.049 485 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.68 % Allowed : 8.66 % 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: 1.16 (0.43), residues: 424 helix: 1.38 (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 0.007 0.001 TRP A 442 HIS 0.004 0.001 HIS A 315 PHE 0.008 0.001 PHE A 193 TYR 0.009 0.001 TYR A 160 ARG 0.002 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: 6 poor density : 23 time to evaluate : 0.522 Fit side-chains REVERT: A 42 ASP cc_start: 0.8822 (t0) cc_final: 0.8546 (t0) REVERT: A 226 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8297 (mp0) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 1.0393 time to fit residues: 26.3002 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 : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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: 0.0570 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 0.0070 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.080031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.065238 restraints weight = 7029.515| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.65 r_work: 0.2706 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3585 Z= 0.162 Angle : 0.521 5.635 4898 Z= 0.263 Chirality : 0.037 0.120 516 Planarity : 0.005 0.046 624 Dihedral : 5.344 59.584 485 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 9.22 % 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: 1.18 (0.43), residues: 424 helix: 1.38 (0.36), residues: 241 sheet: None (None), residues: 0 loop : 0.09 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.008 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 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 31 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.340 Fit side-chains REVERT: A 42 ASP cc_start: 0.8792 (t0) cc_final: 0.8516 (t0) REVERT: A 63 TRP cc_start: 0.9069 (t60) cc_final: 0.8586 (t60) REVERT: A 226 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: A 271 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8270 (mt-10) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.8998 time to fit residues: 26.7179 Evaluate side-chains 28 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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: 0.0040 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.079863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.065248 restraints weight = 7173.420| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.66 r_work: 0.2705 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3585 Z= 0.168 Angle : 0.511 5.528 4898 Z= 0.258 Chirality : 0.037 0.121 516 Planarity : 0.005 0.045 624 Dihedral : 5.088 55.018 485 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 10.61 % Favored : 88.27 % 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: 1.38 (0.36), residues: 241 sheet: 0.29 (1.81), residues: 9 loop : -0.08 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.003 0.001 HIS A 314 PHE 0.009 0.001 PHE A 193 TYR 0.007 0.001 TYR A 85 ARG 0.005 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 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.383 Fit side-chains REVERT: A 42 ASP cc_start: 0.8827 (t0) cc_final: 0.8522 (t0) REVERT: A 63 TRP cc_start: 0.9024 (t60) cc_final: 0.8568 (t60) REVERT: A 226 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: A 271 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8317 (mt-10) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.9168 time to fit residues: 26.1124 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 : 0.418 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.0020 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.080189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.065641 restraints weight = 7205.071| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.65 r_work: 0.2715 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3585 Z= 0.167 Angle : 0.507 5.580 4898 Z= 0.256 Chirality : 0.037 0.121 516 Planarity : 0.005 0.044 624 Dihedral : 4.872 47.800 485 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.84 % Allowed : 11.45 % 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: 1.14 (0.43), residues: 424 helix: 1.39 (0.36), residues: 241 sheet: 0.34 (1.78), residues: 9 loop : -0.02 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.002 0.000 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 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.436 Fit side-chains REVERT: A 42 ASP cc_start: 0.8797 (t0) cc_final: 0.8481 (t0) REVERT: A 63 TRP cc_start: 0.9023 (t60) cc_final: 0.8567 (t60) REVERT: A 226 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: A 271 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8303 (mt-10) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 1.0151 time to fit residues: 28.9209 Evaluate side-chains 29 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.0010 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4524 ------------------------------------------------------------------------------- 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 = 0.3122 r_free = 0.3122 target = 0.081550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.067256 restraints weight = 7069.531| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.65 r_work: 0.2743 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1760 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= 0.158 Angle : 0.509 6.306 4898 Z= 0.255 Chirality : 0.037 0.121 516 Planarity : 0.004 0.044 624 Dihedral : 4.685 43.242 485 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.12 % Allowed : 11.45 % Favored : 87.43 % 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: 1.42 (0.36), residues: 241 sheet: 0.37 (1.79), residues: 9 loop : -0.00 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.002 0.000 HIS A 315 PHE 0.007 0.001 PHE A 193 TYR 0.006 0.001 TYR A 85 ARG 0.003 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 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.376 Fit side-chains REVERT: A 42 ASP cc_start: 0.8813 (t0) cc_final: 0.8495 (t0) REVERT: A 63 TRP cc_start: 0.8996 (t60) cc_final: 0.8517 (t60) REVERT: A 226 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8307 (mp0) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.9004 time to fit residues: 25.6105 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 : 0.423 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.0000 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 = 0.3106 r_free = 0.3106 target = 0.080557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.066123 restraints weight = 7076.887| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.65 r_work: 0.2726 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3585 Z= 0.177 Angle : 0.520 5.617 4898 Z= 0.262 Chirality : 0.037 0.121 516 Planarity : 0.005 0.044 624 Dihedral : 4.676 42.044 485 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.84 % Allowed : 12.29 % Favored : 86.87 % 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: 1.19 (0.43), residues: 424 helix: 1.46 (0.37), residues: 241 sheet: 0.46 (1.80), residues: 9 loop : -0.03 (0.48), residues: 174 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 0.005 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 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.406 Fit side-chains REVERT: A 42 ASP cc_start: 0.8826 (t0) cc_final: 0.8506 (t0) REVERT: A 63 TRP cc_start: 0.9006 (t60) cc_final: 0.8527 (t60) REVERT: A 226 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8272 (mp0) outliers start: 3 outliers final: 2 residues processed: 25 average time/residue: 0.9793 time to fit residues: 25.7960 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 : 0.416 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- 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 = 0.3129 r_free = 0.3129 target = 0.081979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067564 restraints weight = 6940.598| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.65 r_work: 0.2753 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1880 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= 0.161 Angle : 0.501 5.735 4898 Z= 0.253 Chirality : 0.037 0.122 516 Planarity : 0.004 0.044 624 Dihedral : 4.534 36.643 485 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.12 % Allowed : 12.01 % Favored : 86.87 % 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 (0.43), residues: 424 helix: 1.46 (0.37), residues: 241 sheet: 0.47 (1.81), residues: 9 loop : 0.02 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.004 0.001 HIS A 311 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 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.412 Fit side-chains REVERT: A 42 ASP cc_start: 0.8819 (t0) cc_final: 0.8504 (t0) REVERT: A 63 TRP cc_start: 0.8993 (t60) cc_final: 0.8513 (t60) REVERT: A 97 GLN cc_start: 0.8624 (tt0) cc_final: 0.8401 (tt0) REVERT: A 142 LYS cc_start: 0.8418 (mptt) cc_final: 0.8009 (mmtp) REVERT: A 226 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8409 (mt-10) REVERT: A 271 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7936 (tt0) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 1.0932 time to fit residues: 32.0826 Evaluate side-chains 30 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.080007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.065539 restraints weight = 7105.071| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.66 r_work: 0.2711 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3585 Z= 0.192 Angle : 0.533 6.822 4898 Z= 0.267 Chirality : 0.038 0.121 516 Planarity : 0.004 0.044 624 Dihedral : 4.631 34.322 485 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: 1.20 (0.43), residues: 424 helix: 1.58 (0.37), residues: 235 sheet: 0.54 (1.81), residues: 9 loop : -0.17 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 21 HIS 0.004 0.001 HIS A 311 PHE 0.008 0.001 PHE A 193 TYR 0.007 0.001 TYR A 259 ARG 0.002 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 27 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.400 Fit side-chains REVERT: A 42 ASP cc_start: 0.8820 (t0) cc_final: 0.8509 (t0) REVERT: A 63 TRP cc_start: 0.8999 (t60) cc_final: 0.8521 (t60) REVERT: A 226 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: A 271 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8032 (tt0) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 1.0846 time to fit residues: 28.4109 Evaluate side-chains 25 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.081231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066839 restraints weight = 7090.927| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.65 r_work: 0.2740 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3585 Z= 0.167 Angle : 0.517 5.882 4898 Z= 0.261 Chirality : 0.037 0.122 516 Planarity : 0.004 0.044 624 Dihedral : 4.608 29.934 485 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.84 % Allowed : 12.29 % Favored : 86.87 % 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: 1.27 (0.43), residues: 424 helix: 1.47 (0.37), residues: 241 sheet: 0.58 (1.82), residues: 9 loop : 0.08 (0.48), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 116 HIS 0.003 0.001 HIS A 311 PHE 0.011 0.001 PHE A 193 TYR 0.006 0.001 TYR A 85 ARG 0.003 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.74 seconds wall clock time: 36 minutes 48.83 seconds (2208.83 seconds total)