Starting phenix.real_space_refine on Wed Sep 17 05:52:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iwq_60959/09_2025/9iwq_60959.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iwq_60959/09_2025/9iwq_60959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iwq_60959/09_2025/9iwq_60959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iwq_60959/09_2025/9iwq_60959.map" model { file = "/net/cci-nas-00/data/ceres_data/9iwq_60959/09_2025/9iwq_60959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iwq_60959/09_2025/9iwq_60959.cif" } resolution = 2.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 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 S 2 5.16 5 C 1720 2.51 5 N 518 2.21 5 O 613 1.98 5 H 2830 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5683 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 5683 Classifications: {'peptide': 387} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 383} Chain breaks: 1 Time building chain proxies: 1.48, per 1000 atoms: 0.26 Number of scatterers: 5683 At special positions: 0 Unit cell: (88.74, 66.12, 158.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 613 8.00 N 518 7.00 C 1720 6.00 H 2830 1.00 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: 0.56 Conformation dependent library (CDL) restraints added in 168.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 54.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 7 through 34 removed outlier: 3.846A pdb=" N ASN A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 99 removed outlier: 3.737A pdb=" N GLU A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.558A pdb=" N GLU A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 406 through 455 removed outlier: 3.554A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 485 removed outlier: 3.523A pdb=" N SER A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 494 removed outlier: 4.323A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 492 " --> pdb=" O ASN A 488 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 146 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.754A pdb=" N GLY A 322 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR A 311 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP A 320 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 14.746A pdb=" N GLY A 321 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N GLN A 336 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU A 323 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 362 through 364 201 hydrogen bonds defined for protein. 579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 906 1.03 - 1.23: 2096 1.23 - 1.42: 1086 1.42 - 1.62: 1604 1.62 - 1.81: 4 Bond restraints: 5696 Sorted by residual: bond pdb=" CA ASN A 406 " pdb=" CB ASN A 406 " ideal model delta sigma weight residual 1.522 1.461 0.061 7.00e-03 2.04e+04 7.63e+01 bond pdb=" N THR A 6 " pdb=" H THR A 6 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" N ASN A 5 " pdb=" H ASN A 5 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" N GLY A 148 " pdb=" CA GLY A 148 " ideal model delta sigma weight residual 1.444 1.370 0.073 9.10e-03 1.21e+04 6.51e+01 bond pdb=" N GLU A 153 " pdb=" H GLU A 153 " ideal model delta sigma weight residual 0.860 1.013 -0.153 2.00e-02 2.50e+03 5.82e+01 ... (remaining 5691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 7631 2.17 - 4.34: 1833 4.34 - 6.52: 569 6.52 - 8.69: 211 8.69 - 10.86: 17 Bond angle restraints: 10261 Sorted by residual: angle pdb=" CA ASP A 419 " pdb=" CB ASP A 419 " pdb=" CG ASP A 419 " ideal model delta sigma weight residual 112.60 120.28 -7.68 1.00e+00 1.00e+00 5.91e+01 angle pdb=" CA ASN A 5 " pdb=" CB ASN A 5 " pdb=" CG ASN A 5 " ideal model delta sigma weight residual 112.60 119.67 -7.07 1.00e+00 1.00e+00 5.00e+01 angle pdb=" CA ASN A 16 " pdb=" CB ASN A 16 " pdb=" CG ASN A 16 " ideal model delta sigma weight residual 112.60 119.52 -6.92 1.00e+00 1.00e+00 4.79e+01 angle pdb=" CA ASN A 15 " pdb=" CB ASN A 15 " pdb=" CG ASN A 15 " ideal model delta sigma weight residual 112.60 119.50 -6.90 1.00e+00 1.00e+00 4.75e+01 angle pdb=" CA ASN A 406 " pdb=" CB ASN A 406 " pdb=" CG ASN A 406 " ideal model delta sigma weight residual 112.60 119.46 -6.86 1.00e+00 1.00e+00 4.70e+01 ... (remaining 10256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2480 17.80 - 35.61: 109 35.61 - 53.41: 29 53.41 - 71.21: 42 71.21 - 89.01: 5 Dihedral angle restraints: 2665 sinusoidal: 1502 harmonic: 1163 Sorted by residual: dihedral pdb=" N ASN A 5 " pdb=" C ASN A 5 " pdb=" CA ASN A 5 " pdb=" CB ASN A 5 " ideal model delta harmonic sigma weight residual 122.80 134.42 -11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" N LYS A 19 " pdb=" C LYS A 19 " pdb=" CA LYS A 19 " pdb=" CB LYS A 19 " ideal model delta harmonic sigma weight residual 122.80 133.77 -10.97 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C GLU A 153 " pdb=" N GLU A 153 " pdb=" CA GLU A 153 " pdb=" CB GLU A 153 " ideal model delta harmonic sigma weight residual -122.60 -133.38 10.78 0 2.50e+00 1.60e-01 1.86e+01 ... (remaining 2662 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.143: 385 0.143 - 0.285: 20 0.285 - 0.428: 6 0.428 - 0.570: 55 0.570 - 0.713: 13 Chirality restraints: 479 Sorted by residual: chirality pdb=" CG LEU A 11 " pdb=" CB LEU A 11 " pdb=" CD1 LEU A 11 " pdb=" CD2 LEU A 11 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CG LEU A 12 " pdb=" CB LEU A 12 " pdb=" CD1 LEU A 12 " pdb=" CD2 LEU A 12 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB VAL A 147 " pdb=" CA VAL A 147 " pdb=" CG1 VAL A 147 " pdb=" CG2 VAL A 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.41e+00 ... (remaining 476 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " 0.154 2.00e-02 2.50e+03 6.17e-02 1.14e+02 pdb=" CG PHE A 131 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " -0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 131 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 131 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 131 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 131 " 0.011 2.00e-02 2.50e+03 pdb=" HZ PHE A 131 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 175 " -0.038 2.00e-02 2.50e+03 5.19e-02 4.03e+01 pdb=" CD GLN A 175 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN A 175 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 175 " 0.094 2.00e-02 2.50e+03 pdb="HE21 GLN A 175 " -0.013 2.00e-02 2.50e+03 pdb="HE22 GLN A 175 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 388 " 0.078 2.00e-02 2.50e+03 4.17e-02 3.91e+01 pdb=" CG HIS A 388 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS A 388 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS A 388 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 388 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 HIS A 388 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 HIS A 388 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS A 388 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 HIS A 388 " 0.059 2.00e-02 2.50e+03 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 433 2.24 - 2.83: 11360 2.83 - 3.42: 15300 3.42 - 4.01: 19425 4.01 - 4.60: 28464 Nonbonded interactions: 74982 Sorted by model distance: nonbonded pdb=" H ARG A 36 " pdb=" O GLU A 454 " model vdw 1.649 2.450 nonbonded pdb=" HG SER A 104 " pdb=" OD2 ASP A 107 " model vdw 1.656 2.450 nonbonded pdb=" HG SER A 126 " pdb=" O ILE A 162 " model vdw 1.705 2.450 nonbonded pdb=" O VAL A 125 " pdb=" HG1 THR A 129 " model vdw 1.706 2.450 nonbonded pdb=" O GLN A 175 " pdb=" HG1 THR A 403 " model vdw 1.721 2.450 ... (remaining 74977 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: 2.190 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: 0.060 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.010 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 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 : 0.022 0.138 2866 Z= 1.298 Angle : 2.143 10.859 3887 Z= 1.488 Chirality : 0.215 0.713 479 Planarity : 0.010 0.072 522 Dihedral : 12.563 89.014 1046 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 5.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.40), residues: 383 helix: 1.30 (0.32), residues: 204 sheet: -0.34 (0.51), residues: 67 loop : 0.49 (0.62), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 124 TYR 0.071 0.016 TYR A 332 PHE 0.104 0.019 PHE A 131 HIS 0.003 0.002 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.02195 ( 2866) covalent geometry : angle 2.14274 ( 3887) hydrogen bonds : bond 0.15854 ( 201) hydrogen bonds : angle 5.45507 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 29 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.161 Fit side-chains REVERT: A 130 GLN cc_start: 0.8734 (pt0) cc_final: 0.8487 (pp30) REVERT: A 484 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8546 (mm-40) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 1.3962 time to fit residues: 41.4115 Evaluate side-chains 24 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110386 restraints weight = 7264.418| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.19 r_work: 0.3176 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3003 rms_B_bonded: 4.52 restraints_weight: 0.1250 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2866 Z= 0.187 Angle : 0.513 3.694 3887 Z= 0.306 Chirality : 0.039 0.134 479 Planarity : 0.004 0.039 522 Dihedral : 4.896 18.693 407 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.41), residues: 383 helix: 2.88 (0.33), residues: 198 sheet: -0.28 (0.55), residues: 59 loop : 0.64 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 467 TYR 0.011 0.002 TYR A 458 PHE 0.028 0.004 PHE A 131 HIS 0.001 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2866) covalent geometry : angle 0.51331 ( 3887) hydrogen bonds : bond 0.07272 ( 201) hydrogen bonds : angle 4.41629 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 25 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.160 Fit side-chains REVERT: A 130 GLN cc_start: 0.8843 (pt0) cc_final: 0.8485 (pp30) REVERT: A 484 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8292 (mm-40) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 1.4311 time to fit residues: 36.5982 Evaluate side-chains 25 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109367 restraints weight = 7210.675| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.17 r_work: 0.3182 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.3011 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2866 Z= 0.162 Angle : 0.459 3.482 3887 Z= 0.274 Chirality : 0.037 0.137 479 Planarity : 0.003 0.043 522 Dihedral : 4.435 18.204 407 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.32 % Allowed : 5.16 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.43), residues: 383 helix: 3.47 (0.34), residues: 198 sheet: -0.45 (0.55), residues: 59 loop : 0.69 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 422 TYR 0.009 0.001 TYR A 458 PHE 0.027 0.003 PHE A 131 HIS 0.001 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 2866) covalent geometry : angle 0.45884 ( 3887) hydrogen bonds : bond 0.06960 ( 201) hydrogen bonds : angle 4.17583 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 26 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.154 Fit side-chains REVERT: A 484 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8264 (mm-40) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 1.4908 time to fit residues: 38.1268 Evaluate side-chains 25 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110435 restraints weight = 7245.412| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.17 r_work: 0.3185 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.3015 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 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 0.028 2866 Z= 0.153 Angle : 0.443 3.546 3887 Z= 0.261 Chirality : 0.036 0.135 479 Planarity : 0.003 0.040 522 Dihedral : 4.346 21.278 407 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.97 % Allowed : 4.84 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.43), residues: 383 helix: 3.61 (0.34), residues: 198 sheet: -0.49 (0.55), residues: 59 loop : 0.67 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 422 TYR 0.008 0.001 TYR A 458 PHE 0.025 0.003 PHE A 131 HIS 0.001 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2866) covalent geometry : angle 0.44280 ( 3887) hydrogen bonds : bond 0.06794 ( 201) hydrogen bonds : angle 4.10619 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 30 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.131 Fit side-chains REVERT: A 2 GLN cc_start: 0.6847 (mt0) cc_final: 0.6239 (mm110) REVERT: A 484 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8133 (mm-40) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 1.4191 time to fit residues: 40.6884 Evaluate side-chains 27 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112426 restraints weight = 7314.467| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.17 r_work: 0.3194 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3023 rms_B_bonded: 4.53 restraints_weight: 0.1250 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2866 Z= 0.127 Angle : 0.400 3.682 3887 Z= 0.237 Chirality : 0.035 0.133 479 Planarity : 0.003 0.038 522 Dihedral : 4.127 21.188 407 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.97 % Allowed : 5.48 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.44), residues: 383 helix: 3.82 (0.35), residues: 198 sheet: -0.33 (0.56), residues: 57 loop : 0.69 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 422 TYR 0.006 0.001 TYR A 458 PHE 0.019 0.002 PHE A 131 HIS 0.000 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 2866) covalent geometry : angle 0.40037 ( 3887) hydrogen bonds : bond 0.06341 ( 201) hydrogen bonds : angle 3.98716 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 29 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.160 Fit side-chains REVERT: A 2 GLN cc_start: 0.6737 (mt0) cc_final: 0.6226 (mm110) REVERT: A 484 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8016 (mm-40) REVERT: A 488 ASN cc_start: 0.8125 (t0) cc_final: 0.7902 (p0) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 1.4375 time to fit residues: 39.7511 Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 40.0000 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113698 restraints weight = 7241.204| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.17 r_work: 0.3152 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.2977 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2866 Z= 0.126 Angle : 0.397 4.230 3887 Z= 0.233 Chirality : 0.035 0.134 479 Planarity : 0.003 0.037 522 Dihedral : 4.035 21.344 407 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.61 % Allowed : 4.84 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.44), residues: 383 helix: 3.93 (0.35), residues: 198 sheet: -0.36 (0.55), residues: 57 loop : 0.72 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 422 TYR 0.006 0.001 TYR A 458 PHE 0.020 0.002 PHE A 131 HIS 0.000 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 2866) covalent geometry : angle 0.39714 ( 3887) hydrogen bonds : bond 0.06264 ( 201) hydrogen bonds : angle 3.93021 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 31 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.158 Fit side-chains REVERT: A 2 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6284 (mm110) REVERT: A 484 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8001 (mm-40) outliers start: 5 outliers final: 2 residues processed: 28 average time/residue: 1.2030 time to fit residues: 34.5621 Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113558 restraints weight = 7285.204| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.18 r_work: 0.3211 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.3039 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2866 Z= 0.113 Angle : 0.373 4.755 3887 Z= 0.219 Chirality : 0.035 0.133 479 Planarity : 0.002 0.032 522 Dihedral : 3.877 20.108 407 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.97 % Allowed : 5.81 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.44), residues: 383 helix: 4.04 (0.35), residues: 198 sheet: -0.34 (0.56), residues: 57 loop : 0.86 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.005 0.001 TYR A 458 PHE 0.018 0.002 PHE A 131 HIS 0.000 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 2866) covalent geometry : angle 0.37328 ( 3887) hydrogen bonds : bond 0.05924 ( 201) hydrogen bonds : angle 3.85707 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 29 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.139 Fit side-chains REVERT: A 2 GLN cc_start: 0.6527 (mt0) cc_final: 0.6127 (mm110) REVERT: A 484 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7921 (mm-40) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 1.3794 time to fit residues: 38.1509 Evaluate side-chains 27 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112194 restraints weight = 7247.125| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.16 r_work: 0.3163 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.2992 rms_B_bonded: 4.48 restraints_weight: 0.1250 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2866 Z= 0.144 Angle : 0.417 5.177 3887 Z= 0.242 Chirality : 0.036 0.133 479 Planarity : 0.003 0.033 522 Dihedral : 4.056 22.568 407 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.94 % Allowed : 5.16 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.42 (0.44), residues: 383 helix: 3.92 (0.35), residues: 198 sheet: -0.27 (0.56), residues: 57 loop : 0.82 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 422 TYR 0.007 0.001 TYR A 458 PHE 0.020 0.003 PHE A 131 HIS 0.000 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2866) covalent geometry : angle 0.41741 ( 3887) hydrogen bonds : bond 0.06519 ( 201) hydrogen bonds : angle 3.94846 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 31 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.162 Fit side-chains REVERT: A 2 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.6314 (mm110) REVERT: A 484 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8064 (mm-40) outliers start: 6 outliers final: 2 residues processed: 27 average time/residue: 1.3383 time to fit residues: 37.0316 Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110727 restraints weight = 7217.567| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.17 r_work: 0.3181 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3013 rms_B_bonded: 4.47 restraints_weight: 0.1250 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2866 Z= 0.149 Angle : 0.428 5.691 3887 Z= 0.248 Chirality : 0.036 0.133 479 Planarity : 0.003 0.037 522 Dihedral : 4.119 25.195 407 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.29 % Allowed : 5.81 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.44), residues: 383 helix: 3.85 (0.35), residues: 198 sheet: -0.22 (0.56), residues: 57 loop : 0.78 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 422 TYR 0.007 0.001 TYR A 458 PHE 0.022 0.003 PHE A 131 HIS 0.000 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 2866) covalent geometry : angle 0.42821 ( 3887) hydrogen bonds : bond 0.06624 ( 201) hydrogen bonds : angle 3.98571 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 29 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.157 Fit side-chains REVERT: A 2 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6307 (mm110) REVERT: A 484 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8070 (mm-40) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 1.5095 time to fit residues: 40.1924 Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110697 restraints weight = 7285.700| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.19 r_work: 0.3160 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.2984 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2866 Z= 0.123 Angle : 0.401 6.205 3887 Z= 0.231 Chirality : 0.035 0.133 479 Planarity : 0.003 0.037 522 Dihedral : 3.967 23.479 407 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.29 % Allowed : 6.13 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.47 (0.44), residues: 383 helix: 3.96 (0.35), residues: 198 sheet: -0.23 (0.56), residues: 57 loop : 0.83 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.006 0.001 TYR A 458 PHE 0.018 0.002 PHE A 131 HIS 0.000 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 2866) covalent geometry : angle 0.40127 ( 3887) hydrogen bonds : bond 0.06208 ( 201) hydrogen bonds : angle 3.90515 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 343 is missing expected H atoms. Skipping. Evaluate side-chains 28 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.155 Fit side-chains REVERT: A 2 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6298 (mm110) REVERT: A 484 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7967 (mm-40) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 1.5309 time to fit residues: 39.1880 Evaluate side-chains 27 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 139 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111889 restraints weight = 7205.858| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.17 r_work: 0.3130 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.2953 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2866 Z= 0.128 Angle : 0.402 6.020 3887 Z= 0.232 Chirality : 0.035 0.133 479 Planarity : 0.003 0.039 522 Dihedral : 3.926 22.697 407 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 0.97 % Allowed : 6.45 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.44), residues: 383 helix: 3.97 (0.35), residues: 198 sheet: -0.18 (0.56), residues: 57 loop : 0.82 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 422 TYR 0.006 0.001 TYR A 458 PHE 0.020 0.002 PHE A 131 HIS 0.000 0.000 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 2866) covalent geometry : angle 0.40221 ( 3887) hydrogen bonds : bond 0.06248 ( 201) hydrogen bonds : angle 3.89517 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3912.81 seconds wall clock time: 66 minutes 47.35 seconds (4007.35 seconds total)