Starting phenix.real_space_refine on Wed Mar 4 06:46:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qp9_14115/03_2026/7qp9_14115_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qp9_14115/03_2026/7qp9_14115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qp9_14115/03_2026/7qp9_14115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qp9_14115/03_2026/7qp9_14115.map" model { file = "/net/cci-nas-00/data/ceres_data/7qp9_14115/03_2026/7qp9_14115_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qp9_14115/03_2026/7qp9_14115_trim.cif" } resolution = 2.89 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= 0.000 sd= 0.022 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 4 5.49 5 S 34 5.16 5 C 3576 2.51 5 N 804 2.21 5 O 1001 1.98 5 H 5668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 11087 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5245 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5245 Classifications: {'peptide': 327} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'DLP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'DLP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 198 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 183 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 2.10, per 1000 atoms: 0.19 Number of scatterers: 11087 At special positions: 0 Unit cell: (89.933, 88.639, 64.053, 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 4 15.00 O 1001 8.00 N 804 7.00 C 3576 6.00 H 5668 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: 0.67 Conformation dependent library (CDL) restraints added in 387.8 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: 34 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 5 through 30 Proline residue: A 16 - end of helix Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.805A pdb=" N MET A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 91 Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.457A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 164 removed outlier: 4.010A pdb=" N ALA A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.670A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.675A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 273 removed outlier: 3.761A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.842A pdb=" N ALA A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.563A pdb=" N ILE A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'B' and resid 5 through 30 Proline residue: B 16 - end of helix Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.535A pdb=" N GLU B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.760A pdb=" N PHE B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.658A pdb=" N GLY B 97 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 98 " --> pdb=" O PRO B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 121 through 130 removed outlier: 4.427A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 164 removed outlier: 3.987A pdb=" N ALA B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.709A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.672A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 273 removed outlier: 3.756A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.518A pdb=" N PHE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 339 through 367 removed outlier: 3.528A pdb=" N ILE B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix 391 hydrogen bonds defined for protein. 1170 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: 2.72 Time building geometry restraints manager: 0.95 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: 5662 1.03 - 1.23: 15 1.23 - 1.42: 2081 1.42 - 1.61: 3258 1.61 - 1.81: 62 Bond restraints: 11078 Sorted by residual: bond pdb=" O4P DLP B 501 " pdb=" P DLP B 501 " ideal model delta sigma weight residual 1.649 1.595 0.054 2.00e-02 2.50e+03 7.39e+00 bond pdb=" O4P DLP A 502 " pdb=" P DLP A 502 " ideal model delta sigma weight residual 1.649 1.595 0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" O4P DLP A 501 " pdb=" P DLP A 501 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" O4P DLP B 502 " pdb=" P DLP B 502 " ideal model delta sigma weight residual 1.649 1.596 0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" C4 DLP A 502 " pdb=" O4P DLP A 502 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.08e+00 ... (remaining 11073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 19493 2.32 - 4.64: 220 4.64 - 6.96: 10 6.96 - 9.28: 0 9.28 - 11.60: 4 Bond angle restraints: 19727 Sorted by residual: angle pdb=" O3P DLP B 502 " pdb=" P DLP B 502 " pdb=" O4P DLP B 502 " ideal model delta sigma weight residual 93.58 105.18 -11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O3P DLP A 502 " pdb=" P DLP A 502 " pdb=" O4P DLP A 502 " ideal model delta sigma weight residual 93.58 105.17 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" O3P DLP B 501 " pdb=" P DLP B 501 " pdb=" O4P DLP B 501 " ideal model delta sigma weight residual 93.58 103.98 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" O3P DLP A 501 " pdb=" P DLP A 501 " pdb=" O4P DLP A 501 " ideal model delta sigma weight residual 93.58 103.90 -10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" C1 DLP B 501 " pdb=" C2 DLP B 501 " pdb=" O2 DLP B 501 " ideal model delta sigma weight residual 111.29 105.02 6.27 3.00e+00 1.11e-01 4.37e+00 ... (remaining 19722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 4754 23.43 - 46.85: 268 46.85 - 70.28: 72 70.28 - 93.70: 16 93.70 - 117.13: 2 Dihedral angle restraints: 5112 sinusoidal: 2846 harmonic: 2266 Sorted by residual: 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 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA SER A 113 " pdb=" C SER A 113 " pdb=" N VAL A 114 " pdb=" CA VAL A 114 " ideal model delta harmonic sigma weight residual 180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" N DLP B 501 " pdb=" C4 DLP B 501 " pdb=" C5 DLP B 501 " pdb=" O4P DLP B 501 " ideal model delta sinusoidal sigma weight residual 288.95 171.82 117.13 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 744 0.056 - 0.111: 113 0.111 - 0.167: 3 0.167 - 0.223: 2 0.223 - 0.278: 2 Chirality restraints: 864 Sorted by residual: chirality pdb=" C2 DLP A 501 " pdb=" C1 DLP A 501 " pdb=" C3 DLP A 501 " pdb=" O2 DLP A 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.63 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2 DLP B 501 " pdb=" C1 DLP B 501 " pdb=" C3 DLP B 501 " pdb=" O2 DLP B 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2 DLP B 502 " pdb=" C1 DLP B 502 " pdb=" C3 DLP B 502 " pdb=" O2 DLP B 502 " both_signs ideal model delta sigma weight residual False -2.35 -2.57 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 861 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 145 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C GLN A 145 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 145 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 146 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 145 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C GLN B 145 " 0.023 2.00e-02 2.50e+03 pdb=" O GLN B 145 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 146 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 15 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO B 16 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " 0.016 5.00e-02 4.00e+02 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 929 2.22 - 2.82: 24185 2.82 - 3.41: 31632 3.41 - 4.01: 43690 4.01 - 4.60: 67762 Nonbonded interactions: 168198 Sorted by model distance: nonbonded pdb=" HD1 HIS A 237 " pdb=" O TRP A 242 " model vdw 1.629 2.450 nonbonded pdb=" OE1 GLN A 57 " pdb=" HG SER A 256 " model vdw 1.638 2.450 nonbonded pdb=" HD1 HIS B 237 " pdb=" O TRP B 242 " model vdw 1.645 2.450 nonbonded pdb=" O ALA A 354 " pdb=" H THR A 358 " model vdw 1.688 2.450 nonbonded pdb=" O SER B 74 " pdb=" HG SER B 303 " model vdw 1.703 2.450 ... (remaining 168193 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.000 Normalize map: mean=0, sd=1: 6.350 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.700 Find NCS groups from input model: 0.080 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:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 0.054 5410 Z= 0.191 Angle : 0.627 11.603 7308 Z= 0.274 Chirality : 0.039 0.278 864 Planarity : 0.003 0.028 862 Dihedral : 15.528 117.129 2018 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.00 (0.35), residues: 646 helix: 1.94 (0.24), residues: 526 sheet: None (None), residues: 0 loop : -1.49 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 163 TYR 0.005 0.001 TYR A 130 PHE 0.016 0.001 PHE B 330 TRP 0.007 0.001 TRP A 233 HIS 0.001 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5410) covalent geometry : angle 0.62725 ( 7308) hydrogen bonds : bond 0.12800 ( 391) hydrogen bonds : angle 6.27755 ( 1170) *********************** 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 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.307 Fit side-chains REVERT: A 277 ILE cc_start: 0.8899 (tt) cc_final: 0.8654 (tp) REVERT: B 249 ASP cc_start: 0.8063 (t0) cc_final: 0.7807 (t0) REVERT: B 277 ILE cc_start: 0.8903 (tt) cc_final: 0.8662 (tp) outliers start: 0 outliers final: 1 residues processed: 71 average time/residue: 1.0584 time to fit residues: 78.9608 Evaluate side-chains 61 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP 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: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108594 restraints weight = 17123.483| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.75 r_work: 0.3250 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5410 Z= 0.143 Angle : 0.513 4.231 7308 Z= 0.262 Chirality : 0.036 0.127 864 Planarity : 0.004 0.031 862 Dihedral : 15.281 121.247 856 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.54 % Allowed : 6.68 % Favored : 92.78 % 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: 1.92 (0.34), residues: 646 helix: 1.87 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.55 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 99 TYR 0.005 0.001 TYR A 8 PHE 0.017 0.002 PHE B 330 TRP 0.007 0.001 TRP B 233 HIS 0.005 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5410) covalent geometry : angle 0.51258 ( 7308) hydrogen bonds : bond 0.04076 ( 391) hydrogen bonds : angle 4.92595 ( 1170) *********************** 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 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.260 Fit side-chains REVERT: A 228 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7734 (tt) REVERT: A 277 ILE cc_start: 0.8800 (tt) cc_final: 0.8510 (tp) REVERT: B 249 ASP cc_start: 0.8259 (t0) cc_final: 0.7954 (t0) REVERT: B 277 ILE cc_start: 0.8809 (tt) cc_final: 0.8518 (tp) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 1.0524 time to fit residues: 70.9631 Evaluate side-chains 62 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.106250 restraints weight = 17130.984| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.75 r_work: 0.3104 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5410 Z= 0.147 Angle : 0.504 4.296 7308 Z= 0.258 Chirality : 0.036 0.125 864 Planarity : 0.004 0.036 862 Dihedral : 14.691 122.521 854 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.54 % Allowed : 7.40 % Favored : 92.06 % 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: 1.90 (0.34), residues: 646 helix: 1.84 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.38 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.006 0.001 TYR B 361 PHE 0.017 0.002 PHE B 330 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5410) covalent geometry : angle 0.50376 ( 7308) hydrogen bonds : bond 0.03887 ( 391) hydrogen bonds : angle 4.76582 ( 1170) *********************** 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 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.274 Fit side-chains REVERT: A 228 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 250 LYS cc_start: 0.8089 (mttm) cc_final: 0.7788 (mmpt) REVERT: A 277 ILE cc_start: 0.8829 (tt) cc_final: 0.8559 (tp) REVERT: B 91 ARG cc_start: 0.7055 (ttt90) cc_final: 0.6653 (mtp85) REVERT: B 249 ASP cc_start: 0.8361 (t0) cc_final: 0.8046 (t0) REVERT: B 277 ILE cc_start: 0.8807 (tt) cc_final: 0.8538 (tp) outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 1.0761 time to fit residues: 73.5549 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.106014 restraints weight = 17183.569| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.74 r_work: 0.3127 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5410 Z= 0.143 Angle : 0.495 4.308 7308 Z= 0.256 Chirality : 0.036 0.125 864 Planarity : 0.004 0.037 862 Dihedral : 14.508 123.518 854 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.36 % Allowed : 7.22 % Favored : 92.42 % 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: 1.86 (0.34), residues: 646 helix: 1.84 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.50 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 163 TYR 0.006 0.001 TYR B 361 PHE 0.017 0.002 PHE B 330 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5410) covalent geometry : angle 0.49503 ( 7308) hydrogen bonds : bond 0.03679 ( 391) hydrogen bonds : angle 4.64718 ( 1170) *********************** 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 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.280 Fit side-chains REVERT: A 228 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7785 (tt) REVERT: A 277 ILE cc_start: 0.8813 (tt) cc_final: 0.8540 (tp) REVERT: B 91 ARG cc_start: 0.7065 (ttt90) cc_final: 0.6676 (mtp85) REVERT: B 249 ASP cc_start: 0.8373 (t0) cc_final: 0.8064 (t0) REVERT: B 277 ILE cc_start: 0.8807 (tt) cc_final: 0.8538 (tp) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 1.0725 time to fit residues: 71.1018 Evaluate side-chains 62 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 30 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107263 restraints weight = 16897.991| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.64 r_work: 0.3125 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5410 Z= 0.137 Angle : 0.489 4.296 7308 Z= 0.253 Chirality : 0.036 0.125 864 Planarity : 0.004 0.038 862 Dihedral : 14.387 123.131 854 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.72 % Allowed : 7.22 % Favored : 92.06 % 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: 1.87 (0.34), residues: 646 helix: 1.85 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.54 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.006 0.001 TYR B 361 PHE 0.017 0.002 PHE B 330 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5410) covalent geometry : angle 0.48926 ( 7308) hydrogen bonds : bond 0.03633 ( 391) hydrogen bonds : angle 4.57914 ( 1170) *********************** 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 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.235 Fit side-chains REVERT: A 250 LYS cc_start: 0.8086 (mttm) cc_final: 0.7820 (mmpt) REVERT: A 277 ILE cc_start: 0.8835 (tt) cc_final: 0.8588 (tp) REVERT: B 91 ARG cc_start: 0.7113 (ttt90) cc_final: 0.6720 (mtp85) REVERT: B 249 ASP cc_start: 0.8413 (t0) cc_final: 0.8122 (t0) REVERT: B 277 ILE cc_start: 0.8825 (tt) cc_final: 0.8557 (tp) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 1.0697 time to fit residues: 73.0205 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106631 restraints weight = 17191.247| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.68 r_work: 0.3112 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5410 Z= 0.151 Angle : 0.497 4.307 7308 Z= 0.257 Chirality : 0.036 0.125 864 Planarity : 0.004 0.040 862 Dihedral : 14.431 123.431 854 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.54 % Allowed : 7.76 % Favored : 91.70 % 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: 1.81 (0.34), residues: 646 helix: 1.84 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.63 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 308 TYR 0.006 0.001 TYR B 361 PHE 0.018 0.002 PHE A 330 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5410) covalent geometry : angle 0.49747 ( 7308) hydrogen bonds : bond 0.03651 ( 391) hydrogen bonds : angle 4.58239 ( 1170) *********************** 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 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.201 Fit side-chains REVERT: A 91 ARG cc_start: 0.7117 (ttt90) cc_final: 0.6870 (mtp85) REVERT: A 250 LYS cc_start: 0.8078 (mttm) cc_final: 0.7783 (mmpt) REVERT: A 277 ILE cc_start: 0.8828 (tt) cc_final: 0.8581 (tp) REVERT: B 91 ARG cc_start: 0.7118 (ttt90) cc_final: 0.6771 (mtp85) REVERT: B 249 ASP cc_start: 0.8405 (t0) cc_final: 0.8108 (t0) REVERT: B 277 ILE cc_start: 0.8826 (tt) cc_final: 0.8562 (tp) outliers start: 3 outliers final: 2 residues processed: 66 average time/residue: 1.1538 time to fit residues: 79.7490 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105402 restraints weight = 17072.994| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.74 r_work: 0.3083 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5410 Z= 0.150 Angle : 0.501 4.329 7308 Z= 0.259 Chirality : 0.037 0.125 864 Planarity : 0.005 0.040 862 Dihedral : 14.492 123.417 854 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.72 % Allowed : 7.94 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.76 (0.34), residues: 646 helix: 1.80 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.64 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 308 TYR 0.006 0.001 TYR B 361 PHE 0.018 0.002 PHE A 330 TRP 0.008 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5410) covalent geometry : angle 0.50098 ( 7308) hydrogen bonds : bond 0.03666 ( 391) hydrogen bonds : angle 4.57694 ( 1170) *********************** 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 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.230 Fit side-chains REVERT: A 91 ARG cc_start: 0.7113 (ttt90) cc_final: 0.6703 (mtp85) REVERT: A 250 LYS cc_start: 0.8003 (mttm) cc_final: 0.7706 (mmpt) REVERT: A 277 ILE cc_start: 0.8812 (tt) cc_final: 0.8563 (tp) REVERT: B 91 ARG cc_start: 0.7072 (ttt90) cc_final: 0.6714 (mtp85) REVERT: B 249 ASP cc_start: 0.8349 (t0) cc_final: 0.8066 (t0) REVERT: B 277 ILE cc_start: 0.8798 (tt) cc_final: 0.8545 (tp) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 1.1604 time to fit residues: 77.9124 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 88 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 44 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.106464 restraints weight = 17074.964| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.58 r_work: 0.3163 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5410 Z= 0.143 Angle : 0.494 4.293 7308 Z= 0.255 Chirality : 0.037 0.125 864 Planarity : 0.004 0.040 862 Dihedral : 14.530 122.826 854 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.90 % Allowed : 7.94 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.77 (0.34), residues: 646 helix: 1.81 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.66 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 216 TYR 0.006 0.001 TYR B 361 PHE 0.018 0.002 PHE A 330 TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5410) covalent geometry : angle 0.49386 ( 7308) hydrogen bonds : bond 0.03608 ( 391) hydrogen bonds : angle 4.53651 ( 1170) *********************** 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 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.298 Fit side-chains REVERT: A 88 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7589 (mmm) REVERT: A 91 ARG cc_start: 0.7144 (ttt90) cc_final: 0.6713 (mtp85) REVERT: A 277 ILE cc_start: 0.8867 (tt) cc_final: 0.8611 (tp) REVERT: B 91 ARG cc_start: 0.7121 (ttt90) cc_final: 0.6753 (mtp85) REVERT: B 249 ASP cc_start: 0.8391 (t0) cc_final: 0.8090 (t0) REVERT: B 277 ILE cc_start: 0.8831 (tt) cc_final: 0.8579 (tp) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 1.1592 time to fit residues: 77.7205 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.0470 chunk 51 optimal weight: 0.0980 chunk 57 optimal weight: 0.5980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109259 restraints weight = 16901.097| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.55 r_work: 0.3017 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5410 Z= 0.098 Angle : 0.463 4.154 7308 Z= 0.238 Chirality : 0.036 0.135 864 Planarity : 0.004 0.039 862 Dihedral : 14.056 118.064 854 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.72 % Allowed : 7.94 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.02 (0.34), residues: 646 helix: 2.02 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.69 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 216 TYR 0.005 0.001 TYR B 18 PHE 0.015 0.001 PHE B 330 TRP 0.007 0.001 TRP B 233 HIS 0.002 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 5410) covalent geometry : angle 0.46292 ( 7308) hydrogen bonds : bond 0.03323 ( 391) hydrogen bonds : angle 4.38291 ( 1170) *********************** 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 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.176 Fit side-chains REVERT: A 91 ARG cc_start: 0.7049 (ttt90) cc_final: 0.6773 (mtp85) REVERT: A 250 LYS cc_start: 0.7875 (mttm) cc_final: 0.7618 (mmpt) REVERT: A 277 ILE cc_start: 0.8781 (tt) cc_final: 0.8533 (tp) REVERT: B 88 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7553 (mmm) REVERT: B 91 ARG cc_start: 0.7000 (ttt90) cc_final: 0.6632 (mtp85) REVERT: B 249 ASP cc_start: 0.8132 (t0) cc_final: 0.7872 (t0) REVERT: B 277 ILE cc_start: 0.8786 (tt) cc_final: 0.8532 (tp) outliers start: 4 outliers final: 3 residues processed: 64 average time/residue: 1.2309 time to fit residues: 82.3908 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.108006 restraints weight = 17057.176| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.58 r_work: 0.2996 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5410 Z= 0.126 Angle : 0.483 4.494 7308 Z= 0.247 Chirality : 0.036 0.139 864 Planarity : 0.004 0.039 862 Dihedral : 14.057 117.512 854 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.90 % Allowed : 8.12 % Favored : 90.97 % 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: 2.00 (0.34), residues: 646 helix: 1.99 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.69 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 216 TYR 0.005 0.001 TYR B 361 PHE 0.017 0.001 PHE A 330 TRP 0.007 0.001 TRP B 233 HIS 0.002 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5410) covalent geometry : angle 0.48262 ( 7308) hydrogen bonds : bond 0.03417 ( 391) hydrogen bonds : angle 4.41716 ( 1170) ********************** 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 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.275 Fit side-chains REVERT: A 88 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7496 (mmm) REVERT: A 91 ARG cc_start: 0.7055 (ttt90) cc_final: 0.6774 (mtp85) REVERT: A 277 ILE cc_start: 0.8770 (tt) cc_final: 0.8526 (tp) REVERT: B 88 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: B 91 ARG cc_start: 0.7006 (ttt90) cc_final: 0.6636 (mtp85) REVERT: B 249 ASP cc_start: 0.8208 (t0) cc_final: 0.7927 (t0) REVERT: B 277 ILE cc_start: 0.8776 (tt) cc_final: 0.8529 (tp) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 1.2011 time to fit residues: 79.1551 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.107124 restraints weight = 17055.434| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.58 r_work: 0.2985 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5410 Z= 0.141 Angle : 0.499 5.237 7308 Z= 0.256 Chirality : 0.037 0.142 864 Planarity : 0.004 0.039 862 Dihedral : 14.126 117.673 854 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.90 % Allowed : 8.12 % Favored : 90.97 % 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: 1.88 (0.34), residues: 646 helix: 1.89 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.67 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 308 TYR 0.006 0.001 TYR B 361 PHE 0.018 0.002 PHE A 330 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5410) covalent geometry : angle 0.49891 ( 7308) hydrogen bonds : bond 0.03561 ( 391) hydrogen bonds : angle 4.47095 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.88 seconds wall clock time: 61 minutes 7.55 seconds (3667.55 seconds total)