Starting phenix.real_space_refine on Wed Mar 4 05:45:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qpa_14116/03_2026/7qpa_14116_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qpa_14116/03_2026/7qpa_14116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qpa_14116/03_2026/7qpa_14116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qpa_14116/03_2026/7qpa_14116.map" model { file = "/net/cci-nas-00/data/ceres_data/7qpa_14116/03_2026/7qpa_14116_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qpa_14116/03_2026/7qpa_14116_trim.cif" } resolution = 3.18 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= 0.001 sd= 0.047 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 34 5.16 5 C 3508 2.51 5 N 804 2.21 5 O 926 1.98 5 H 5540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10814 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5244 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5244 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'DLP': 2, 'IAC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 87 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 105 Classifications: {'water': 35} Link IDs: {None: 34} Time building chain proxies: 2.08, per 1000 atoms: 0.19 Number of scatterers: 10814 At special positions: 0 Unit cell: (76.346, 100.932, 67.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 2 15.00 O 926 8.00 N 804 7.00 C 3508 6.00 H 5540 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: 0.92 Conformation dependent library (CDL) restraints added in 332.7 milliseconds 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 87.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 3 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 51 through 61 removed outlier: 3.866A pdb=" N GLN A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.534A pdb=" N PHE A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.726A pdb=" N ARG A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.676A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.938A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.674A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.906A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.915A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 274 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.777A pdb=" N ILE A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 351 removed outlier: 4.108A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 367 removed outlier: 4.043A pdb=" N LEU A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 29 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 51 through 61 removed outlier: 3.846A pdb=" N GLN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.781A pdb=" N MET B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.686A pdb=" N PHE B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.536A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 148 removed outlier: 4.046A pdb=" N SER B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.688A pdb=" N LEU B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.660A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.945A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 274 Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.687A pdb=" N ILE B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.798A pdb=" N THR B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 367 removed outlier: 4.070A pdb=" N LEU B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1134 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: 2.16 Time building geometry restraints manager: 1.30 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: 5534 1.03 - 1.23: 13 1.23 - 1.42: 2091 1.42 - 1.62: 3172 1.62 - 1.81: 62 Bond restraints: 10872 Sorted by residual: bond pdb=" N IAC A 401 " pdb=" C8 IAC A 401 " ideal model delta sigma weight residual 1.371 1.315 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" N IAC B 401 " pdb=" C8 IAC B 401 " ideal model delta sigma weight residual 1.371 1.315 0.056 2.00e-02 2.50e+03 7.76e+00 bond pdb=" O4P DLP A 402 " pdb=" P DLP A 402 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O4P DLP A 403 " pdb=" P DLP A 403 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C4 DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sigma weight residual 1.409 1.450 -0.041 2.00e-02 2.50e+03 4.11e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19377 2.09 - 4.18: 183 4.18 - 6.27: 10 6.27 - 8.36: 4 8.36 - 10.45: 2 Bond angle restraints: 19576 Sorted by residual: angle pdb=" O3P DLP A 403 " pdb=" P DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sigma weight residual 93.58 104.03 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O3P DLP A 402 " pdb=" P DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sigma weight residual 93.58 103.82 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N VAL A 106 " pdb=" CA VAL A 106 " pdb=" C VAL A 106 " ideal model delta sigma weight residual 113.00 109.51 3.49 1.30e+00 5.92e-01 7.20e+00 angle pdb=" N ILE B 318 " pdb=" CA ILE B 318 " pdb=" C ILE B 318 " ideal model delta sigma weight residual 112.96 110.36 2.60 1.00e+00 1.00e+00 6.78e+00 angle pdb=" C18 IAC A 401 " pdb=" C17 IAC A 401 " pdb=" C7 IAC A 401 " ideal model delta sigma weight residual 115.88 109.02 6.86 3.00e+00 1.11e-01 5.23e+00 ... (remaining 19571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 4688 23.15 - 46.30: 260 46.30 - 69.45: 70 69.45 - 92.60: 8 92.60 - 115.75: 2 Dihedral angle restraints: 5028 sinusoidal: 2762 harmonic: 2266 Sorted by residual: dihedral pdb=" N DLP A 403 " pdb=" C4 DLP A 403 " pdb=" C5 DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sinusoidal sigma weight residual 288.95 173.20 115.75 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" N DLP A 402 " pdb=" C4 DLP A 402 " pdb=" C5 DLP A 402 " pdb=" O4P DLP A 402 " ideal model delta sinusoidal sigma weight residual 288.95 174.87 114.08 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA SER B 113 " pdb=" C SER B 113 " pdb=" N VAL B 114 " pdb=" CA VAL B 114 " ideal model delta harmonic sigma weight residual 180.00 -162.86 -17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 637 0.040 - 0.079: 189 0.079 - 0.119: 30 0.119 - 0.159: 3 0.159 - 0.199: 3 Chirality restraints: 862 Sorted by residual: chirality pdb=" C2 DLP A 403 " pdb=" C1 DLP A 403 " pdb=" C3 DLP A 403 " pdb=" O2 DLP A 403 " both_signs ideal model delta sigma weight residual False -2.35 -2.55 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" C2 DLP A 402 " pdb=" C1 DLP A 402 " pdb=" C3 DLP A 402 " pdb=" O2 DLP A 402 " both_signs ideal model delta sigma weight residual False -2.35 -2.55 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CG LEU B 5 " pdb=" CB LEU B 5 " pdb=" CD1 LEU B 5 " pdb=" CD2 LEU B 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 859 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 68 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 69 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 328 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 329 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 216 " 0.136 9.50e-02 1.11e+02 4.56e-02 2.57e+00 pdb=" NE ARG A 216 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 216 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 216 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 216 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 216 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 216 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 216 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 216 " 0.000 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 62 2.04 - 2.68: 16669 2.68 - 3.32: 33261 3.32 - 3.96: 42515 3.96 - 4.60: 66955 Nonbonded interactions: 159462 Sorted by model distance: nonbonded pdb="HD21 LEU B 5 " pdb=" HE1 HIS B 9 " model vdw 1.404 2.270 nonbonded pdb="HD21 ASN A 117 " pdb=" O HOH A 501 " model vdw 1.644 2.450 nonbonded pdb="HD21 ASN B 117 " pdb=" O HOH B 501 " model vdw 1.647 2.450 nonbonded pdb=" OD1 ASN A 63 " pdb=" H PHE A 65 " model vdw 1.667 2.450 nonbonded pdb=" HZ3 LYS B 334 " pdb=" O HOH B 503 " model vdw 1.707 2.450 ... (remaining 159457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 0 through 401) selection = chain 'B' } 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: 0.010 Normalize map: mean=0, sd=1: 0.650 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 0.056 5332 Z= 0.204 Angle : 0.638 10.454 7224 Z= 0.310 Chirality : 0.038 0.199 862 Planarity : 0.005 0.060 854 Dihedral : 15.169 115.750 1936 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.33), residues: 646 helix: 1.66 (0.23), residues: 506 sheet: None (None), residues: 0 loop : -1.71 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 216 TYR 0.007 0.001 TYR B 8 PHE 0.015 0.001 PHE A 330 TRP 0.025 0.001 TRP A 93 HIS 0.010 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 5332) covalent geometry : angle 0.63780 ( 7224) hydrogen bonds : bond 0.12476 ( 379) hydrogen bonds : angle 6.73809 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.271 Fit side-chains REVERT: A 67 MET cc_start: 0.8539 (mtm) cc_final: 0.8321 (mtp) REVERT: A 308 ARG cc_start: 0.7457 (mmt-90) cc_final: 0.7256 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1567 time to fit residues: 19.1293 Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.166793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137546 restraints weight = 16628.929| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.76 r_work: 0.3369 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5332 Z= 0.153 Angle : 0.555 5.158 7224 Z= 0.288 Chirality : 0.037 0.124 862 Planarity : 0.005 0.046 854 Dihedral : 11.641 104.937 772 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 5.42 % Favored : 93.86 % 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 are not related in a simple way. whole: 1.13 (0.33), residues: 646 helix: 1.40 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.04 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 216 TYR 0.007 0.001 TYR B 8 PHE 0.016 0.001 PHE A 330 TRP 0.010 0.001 TRP B 233 HIS 0.009 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5332) covalent geometry : angle 0.55526 ( 7224) hydrogen bonds : bond 0.04244 ( 379) hydrogen bonds : angle 5.47814 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.244 Fit side-chains REVERT: A 67 MET cc_start: 0.8648 (mtm) cc_final: 0.8420 (mtp) REVERT: A 208 MET cc_start: 0.6896 (tpp) cc_final: 0.6474 (tpt) REVERT: B 308 ARG cc_start: 0.7407 (mmt-90) cc_final: 0.7065 (mmt-90) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.1576 time to fit residues: 17.2379 Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.166674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137473 restraints weight = 16786.019| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.75 r_work: 0.3352 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5332 Z= 0.155 Angle : 0.540 5.002 7224 Z= 0.279 Chirality : 0.037 0.127 862 Planarity : 0.005 0.048 854 Dihedral : 11.438 98.584 772 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 6.68 % Favored : 92.60 % 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 are not related in a simple way. whole: 0.98 (0.33), residues: 646 helix: 1.33 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.007 0.001 TYR B 8 PHE 0.016 0.001 PHE A 330 TRP 0.010 0.001 TRP B 233 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5332) covalent geometry : angle 0.53998 ( 7224) hydrogen bonds : bond 0.03911 ( 379) hydrogen bonds : angle 5.23186 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.319 Fit side-chains REVERT: A 208 MET cc_start: 0.6811 (tpp) cc_final: 0.6439 (tpt) REVERT: B 308 ARG cc_start: 0.7410 (mmt-90) cc_final: 0.7077 (mmt-90) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.1703 time to fit residues: 17.3589 Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.165641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134810 restraints weight = 16791.646| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.90 r_work: 0.3321 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5332 Z= 0.148 Angle : 0.534 5.059 7224 Z= 0.275 Chirality : 0.036 0.126 862 Planarity : 0.005 0.047 854 Dihedral : 11.447 92.832 772 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 7.76 % Favored : 91.52 % 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 are not related in a simple way. whole: 0.98 (0.33), residues: 646 helix: 1.34 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.32 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 216 TYR 0.006 0.001 TYR B 361 PHE 0.015 0.001 PHE A 330 TRP 0.010 0.001 TRP B 233 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5332) covalent geometry : angle 0.53423 ( 7224) hydrogen bonds : bond 0.03651 ( 379) hydrogen bonds : angle 5.08804 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.287 Fit side-chains REVERT: A 208 MET cc_start: 0.6715 (tpp) cc_final: 0.6364 (tpt) outliers start: 4 outliers final: 4 residues processed: 82 average time/residue: 0.1731 time to fit residues: 18.5593 Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135139 restraints weight = 16734.716| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.77 r_work: 0.3327 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5332 Z= 0.171 Angle : 0.551 5.036 7224 Z= 0.284 Chirality : 0.037 0.175 862 Planarity : 0.005 0.046 854 Dihedral : 11.656 87.743 772 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.08 % Allowed : 8.84 % Favored : 90.07 % 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 are not related in a simple way. whole: 0.89 (0.33), residues: 646 helix: 1.29 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.40 (0.47), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 308 TYR 0.007 0.001 TYR B 361 PHE 0.015 0.001 PHE A 330 TRP 0.011 0.001 TRP B 233 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5332) covalent geometry : angle 0.55071 ( 7224) hydrogen bonds : bond 0.03712 ( 379) hydrogen bonds : angle 5.06015 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.275 Fit side-chains REVERT: A 208 MET cc_start: 0.6783 (tpp) cc_final: 0.6438 (tpt) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.1672 time to fit residues: 17.3601 Evaluate side-chains 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain B residue 12 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135771 restraints weight = 16823.635| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.78 r_work: 0.3332 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5332 Z= 0.142 Angle : 0.524 4.957 7224 Z= 0.271 Chirality : 0.037 0.163 862 Planarity : 0.005 0.048 854 Dihedral : 11.527 86.228 772 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.90 % Allowed : 9.39 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.33), residues: 646 helix: 1.34 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.37 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.006 0.001 TYR B 361 PHE 0.014 0.001 PHE A 330 TRP 0.011 0.001 TRP B 233 HIS 0.005 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5332) covalent geometry : angle 0.52409 ( 7224) hydrogen bonds : bond 0.03552 ( 379) hydrogen bonds : angle 4.97874 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.167 Fit side-chains REVERT: A 208 MET cc_start: 0.6786 (tpp) cc_final: 0.6446 (tpt) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.1664 time to fit residues: 16.1197 Evaluate side-chains 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN 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 = 0.165710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135948 restraints weight = 16787.200| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.80 r_work: 0.3342 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5332 Z= 0.145 Angle : 0.524 4.922 7224 Z= 0.271 Chirality : 0.037 0.126 862 Planarity : 0.005 0.045 854 Dihedral : 11.420 87.677 772 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.90 % Allowed : 9.57 % Favored : 89.53 % 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 are not related in a simple way. whole: 0.96 (0.33), residues: 646 helix: 1.29 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.24 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.006 0.001 TYR A 361 PHE 0.014 0.001 PHE A 330 TRP 0.011 0.001 TRP B 233 HIS 0.005 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5332) covalent geometry : angle 0.52423 ( 7224) hydrogen bonds : bond 0.03511 ( 379) hydrogen bonds : angle 4.94275 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.218 Fit side-chains REVERT: A 208 MET cc_start: 0.6772 (tpp) cc_final: 0.6439 (tpt) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.1659 time to fit residues: 15.5237 Evaluate side-chains 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137447 restraints weight = 16708.964| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.77 r_work: 0.3344 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5332 Z= 0.130 Angle : 0.511 4.764 7224 Z= 0.263 Chirality : 0.036 0.126 862 Planarity : 0.005 0.045 854 Dihedral : 11.205 87.422 772 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.62 % Allowed : 9.39 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.33), residues: 646 helix: 1.37 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.23 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.006 0.001 TYR A 361 PHE 0.015 0.001 PHE A 155 TRP 0.010 0.001 TRP B 233 HIS 0.007 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5332) covalent geometry : angle 0.51104 ( 7224) hydrogen bonds : bond 0.03379 ( 379) hydrogen bonds : angle 4.86153 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.230 Fit side-chains REVERT: A 208 MET cc_start: 0.6781 (tpp) cc_final: 0.6450 (tpt) REVERT: A 308 ARG cc_start: 0.7259 (mmt-90) cc_final: 0.6294 (mtm180) REVERT: B 9 HIS cc_start: 0.7723 (OUTLIER) cc_final: 0.7136 (t-90) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.1711 time to fit residues: 17.4167 Evaluate side-chains 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.137124 restraints weight = 16663.546| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.78 r_work: 0.3344 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5332 Z= 0.138 Angle : 0.516 4.671 7224 Z= 0.266 Chirality : 0.036 0.126 862 Planarity : 0.005 0.044 854 Dihedral : 11.166 87.463 772 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.44 % Allowed : 9.57 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.33), residues: 646 helix: 1.34 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.45 (0.46), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 308 TYR 0.006 0.001 TYR B 130 PHE 0.014 0.001 PHE A 330 TRP 0.010 0.001 TRP B 233 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5332) covalent geometry : angle 0.51572 ( 7224) hydrogen bonds : bond 0.03400 ( 379) hydrogen bonds : angle 4.85734 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.264 Fit side-chains REVERT: A 208 MET cc_start: 0.6768 (tpp) cc_final: 0.6439 (tpt) REVERT: A 308 ARG cc_start: 0.7254 (mmt-90) cc_final: 0.6286 (mtm180) REVERT: B 9 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7132 (t-90) REVERT: B 18 TYR cc_start: 0.8959 (m-80) cc_final: 0.8654 (m-80) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.1823 time to fit residues: 18.1175 Evaluate side-chains 79 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.165680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135828 restraints weight = 16699.074| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.80 r_work: 0.3329 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5332 Z= 0.154 Angle : 0.533 4.707 7224 Z= 0.275 Chirality : 0.037 0.126 862 Planarity : 0.005 0.044 854 Dihedral : 11.046 88.493 772 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.26 % Allowed : 9.57 % Favored : 89.17 % 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 are not related in a simple way. whole: 0.89 (0.33), residues: 646 helix: 1.28 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.52 (0.46), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 308 TYR 0.007 0.001 TYR A 361 PHE 0.016 0.001 PHE A 155 TRP 0.011 0.001 TRP B 233 HIS 0.006 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5332) covalent geometry : angle 0.53276 ( 7224) hydrogen bonds : bond 0.03481 ( 379) hydrogen bonds : angle 4.89166 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1292 Ramachandran restraints generated. 646 Oldfield, 0 Emsley, 646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.261 Fit side-chains REVERT: A 9 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7166 (t-90) REVERT: A 208 MET cc_start: 0.6758 (tpp) cc_final: 0.6428 (tpt) REVERT: A 308 ARG cc_start: 0.7261 (mmt-90) cc_final: 0.6287 (mtm180) REVERT: B 9 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7122 (t-90) REVERT: B 18 TYR cc_start: 0.8968 (m-80) cc_final: 0.8648 (m-80) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.1818 time to fit residues: 18.5063 Evaluate side-chains 80 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain B residue 9 HIS Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN 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 = 0.166587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136812 restraints weight = 16648.977| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.80 r_work: 0.3342 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5332 Z= 0.133 Angle : 0.514 4.604 7224 Z= 0.265 Chirality : 0.036 0.161 862 Planarity : 0.006 0.068 854 Dihedral : 10.729 86.219 772 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.44 % Allowed : 9.57 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.33), residues: 646 helix: 1.35 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -2.48 (0.46), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 216 TYR 0.006 0.001 TYR A 361 PHE 0.013 0.001 PHE A 330 TRP 0.011 0.001 TRP B 233 HIS 0.007 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5332) covalent geometry : angle 0.51370 ( 7224) hydrogen bonds : bond 0.03357 ( 379) hydrogen bonds : angle 4.84598 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2936.69 seconds wall clock time: 50 minutes 19.89 seconds (3019.89 seconds total)