Starting phenix.real_space_refine on Fri Oct 23 00:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zdy_74078/10_2026/9zdy_74078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zdy_74078/10_2026/9zdy_74078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zdy_74078/10_2026/9zdy_74078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zdy_74078/10_2026/9zdy_74078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zdy_74078/10_2026/9zdy_74078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zdy_74078/10_2026/9zdy_74078.map" } resolution = 3.9 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 4 5.16 5 C 2287 2.51 5 N 587 2.21 5 O 695 1.98 5 H 3469 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7042 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1764 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1764 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1764 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1750 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.30, per 1000 atoms: 0.18 Number of scatterers: 7042 At special positions: 0 Unit cell: (79.679, 81.141, 61.404, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 695 8.00 N 587 7.00 C 2287 6.00 H 3469 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: 0.61 Conformation dependent library (CDL) restraints added in 258.6 milliseconds 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 6 sheets defined 7.6% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'C' and resid 74 through 82 removed outlier: 4.348A pdb=" N ALA C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU C 82 " --> pdb=" O TYR C 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 81 removed outlier: 3.637A pdb=" N TYR D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.622A pdb=" N SER A 23 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 14 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.622A pdb=" N SER A 23 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 23 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 48 removed outlier: 6.684A pdb=" N VAL A 32 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 46 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 30 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 48 removed outlier: 6.717A pdb=" N VAL B 32 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N SER B 46 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL B 30 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.529A pdb=" N VAL C 32 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER C 46 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 30 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL D 94 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA C 91 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N GLU D 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 45 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.82 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: 3469 1.03 - 1.22: 0 1.22 - 1.42: 1554 1.42 - 1.61: 2106 1.61 - 1.80: 8 Bond restraints: 7137 Sorted by residual: bond pdb=" N CYS C 10 " pdb=" CA CYS C 10 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.30e+00 bond pdb=" N CYS B 10 " pdb=" CA CYS B 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N CYS D 10 " pdb=" CA CYS D 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N CYS A 10 " pdb=" CA CYS A 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" CB LYS A 80 " pdb=" CG LYS A 80 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.62e+00 ... (remaining 7132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.34: 12884 7.34 - 14.69: 3 14.69 - 22.03: 0 22.03 - 29.38: 0 29.38 - 36.72: 3 Bond angle restraints: 12890 Sorted by residual: angle pdb=" C ARG D 103 " pdb=" CA ARG D 103 " pdb=" HA ARG D 103 " ideal model delta sigma weight residual 109.00 72.28 36.72 3.00e+00 1.11e-01 1.50e+02 angle pdb=" N ARG D 103 " pdb=" CA ARG D 103 " pdb=" HA ARG D 103 " ideal model delta sigma weight residual 110.00 74.15 35.85 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CB ARG D 103 " pdb=" CA ARG D 103 " pdb=" HA ARG D 103 " ideal model delta sigma weight residual 109.00 76.88 32.12 3.00e+00 1.11e-01 1.15e+02 angle pdb=" N ARG D 103 " pdb=" CA ARG D 103 " pdb=" C ARG D 103 " ideal model delta sigma weight residual 109.24 122.19 -12.95 1.51e+00 4.39e-01 7.35e+01 angle pdb=" CA LYS A 80 " pdb=" CB LYS A 80 " pdb=" CG LYS A 80 " ideal model delta sigma weight residual 114.10 123.14 -9.04 2.00e+00 2.50e-01 2.04e+01 ... (remaining 12885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 2961 15.46 - 30.91: 265 30.91 - 46.37: 97 46.37 - 61.82: 69 61.82 - 77.28: 19 Dihedral angle restraints: 3411 sinusoidal: 1786 harmonic: 1625 Sorted by residual: dihedral pdb=" CA ALA C 97 " pdb=" C ALA C 97 " pdb=" N ASN C 98 " pdb=" CA ASN C 98 " ideal model delta harmonic sigma weight residual 180.00 -154.15 -25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ASN C 98 " pdb=" C ASN C 98 " pdb=" N ASP C 99 " pdb=" CA ASP C 99 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 468 0.067 - 0.134: 96 0.134 - 0.202: 6 0.202 - 0.269: 0 0.269 - 0.336: 1 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA ARG D 103 " pdb=" N ARG D 103 " pdb=" C ARG D 103 " pdb=" CB ARG D 103 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA PRO D 102 " pdb=" N PRO D 102 " pdb=" C PRO D 102 " pdb=" CB PRO D 102 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA VAL C 93 " pdb=" N VAL C 93 " pdb=" C VAL C 93 " pdb=" CB VAL C 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 568 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 80 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LYS A 80 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS A 80 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 81 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 27 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ASN B 27 " 0.026 2.00e-02 2.50e+03 pdb=" O ASN B 27 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 28 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 92 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" CD GLU B 92 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU B 92 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU B 92 " -0.008 2.00e-02 2.50e+03 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 216 2.15 - 2.76: 13244 2.76 - 3.38: 19126 3.38 - 3.99: 25062 3.99 - 4.60: 38381 Nonbonded interactions: 96029 Sorted by model distance: nonbonded pdb=" H ARG D 103 " pdb=" HA ARG D 103 " model vdw 1.541 1.816 nonbonded pdb=" OD2 ASP D 99 " pdb=" HE ARG D 103 " model vdw 1.567 2.450 nonbonded pdb=" HA ARG D 103 " pdb=" HB2 ARG D 103 " model vdw 1.636 1.952 nonbonded pdb=" HB2 LYS C 15 " pdb=" HZ3 LYS C 15 " model vdw 1.761 2.270 nonbonded pdb=" HB3 LYS A 15 " pdb=" HZ1 LYS A 15 " model vdw 1.776 2.270 ... (remaining 96024 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 10 through 124) selection = (chain 'B' and resid 10 through 124) selection = (chain 'C' and resid 10 through 124) selection = chain 'D' } 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 group one per residue 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: 1.110 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 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 0.049 3668 Z= 0.184 Angle : 0.792 12.946 5008 Z= 0.427 Chirality : 0.054 0.336 571 Planarity : 0.005 0.040 638 Dihedral : 13.913 69.460 1284 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % 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: -0.04 (0.37), residues: 455 helix: -1.40 (0.81), residues: 33 sheet: 1.53 (0.36), residues: 199 loop : -1.36 (0.36), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 21 TYR 0.012 0.002 TYR A 114 PHE 0.014 0.002 PHE D 87 TRP 0.012 0.002 TRP A 79 HIS 0.004 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 3668) covalent geometry : angle 0.79167 / 0.43 ( 5008) hydrogen bonds : bond 0.17358 / 12.40 ( 132) hydrogen bonds : angle 8.86239 / 6.35 ( 363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8808 (tptp) cc_final: 0.8110 (ttmm) REVERT: B 15 LYS cc_start: 0.7525 (ttmm) cc_final: 0.7240 (ttmt) REVERT: C 104 ARG cc_start: 0.5120 (ttt180) cc_final: 0.3858 (mtt180) REVERT: C 105 TYR cc_start: 0.8048 (m-10) cc_final: 0.7779 (m-10) REVERT: C 116 TYR cc_start: 0.8672 (p90) cc_final: 0.8342 (p90) REVERT: D 68 ILE cc_start: 0.8103 (mt) cc_final: 0.7654 (tt) REVERT: D 72 GLU cc_start: 0.8247 (tt0) cc_final: 0.7989 (tp30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1067 time to fit residues: 18.5664 Evaluate side-chains 113 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 37] chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.192546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.173946 restraints weight = 12142.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.180320 restraints weight = 6006.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.184612 restraints weight = 3300.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.187343 restraints weight = 1947.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.189052 restraints weight = 1203.912| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3668 Z= 0.178 Angle : 0.684 7.387 5008 Z= 0.369 Chirality : 0.054 0.408 571 Planarity : 0.005 0.037 638 Dihedral : 6.062 22.539 495 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.13 % Allowed : 16.71 % Favored : 80.16 % Cbeta Deviations : 0.23 % 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: -0.13 (0.38), residues: 455 helix: -1.05 (0.83), residues: 33 sheet: 1.45 (0.35), residues: 209 loop : -1.63 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.015 0.002 TYR D 69 PHE 0.016 0.002 PHE C 95 TRP 0.010 0.001 TRP C 41 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 3668) covalent geometry : angle 0.68357 / 0.37 ( 5008) hydrogen bonds : bond 0.03989 / 2.69 ( 132) hydrogen bonds : angle 6.49000 / 4.56 ( 363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 SER cc_start: 0.9062 (m) cc_final: 0.8808 (m) REVERT: B 116 TYR cc_start: 0.8894 (p90) cc_final: 0.8420 (p90) REVERT: C 104 ARG cc_start: 0.5492 (ttt180) cc_final: 0.4022 (mtt180) REVERT: D 68 ILE cc_start: 0.8545 (mt) cc_final: 0.8168 (tt) outliers start: 12 outliers final: 7 residues processed: 120 average time/residue: 0.1133 time to fit residues: 17.4471 Evaluate side-chains 117 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 98 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [39, 1, 27, 41, 6, 20, 24, 23, 15, 8, 35] chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.192440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.173224 restraints weight = 12054.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.179763 restraints weight = 6093.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.183999 restraints weight = 3426.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.186768 restraints weight = 2078.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.188600 restraints weight = 1324.163| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3668 Z= 0.127 Angle : 0.602 5.678 5008 Z= 0.321 Chirality : 0.052 0.381 571 Planarity : 0.004 0.039 638 Dihedral : 5.560 22.546 495 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.09 % Allowed : 18.02 % Favored : 79.90 % Cbeta Deviations : 0.23 % 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: -0.22 (0.38), residues: 455 helix: -0.56 (0.91), residues: 33 sheet: 1.41 (0.36), residues: 204 loop : -1.73 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 21 TYR 0.008 0.001 TYR D 69 PHE 0.012 0.002 PHE A 87 TRP 0.007 0.001 TRP C 41 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 3668) covalent geometry : angle 0.60234 / 0.32 ( 5008) hydrogen bonds : bond 0.03679 / 2.44 ( 132) hydrogen bonds : angle 6.14191 / 4.29 ( 363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 SER cc_start: 0.9154 (m) cc_final: 0.8913 (m) REVERT: B 69 TYR cc_start: 0.7691 (m-80) cc_final: 0.7468 (m-80) REVERT: B 116 TYR cc_start: 0.8861 (p90) cc_final: 0.8394 (p90) REVERT: C 27 ASN cc_start: 0.5855 (OUTLIER) cc_final: 0.5339 (p0) REVERT: C 104 ARG cc_start: 0.5487 (ttt180) cc_final: 0.3970 (mtt180) REVERT: D 68 ILE cc_start: 0.8557 (mt) cc_final: 0.8149 (tt) outliers start: 8 outliers final: 5 residues processed: 111 average time/residue: 0.0972 time to fit residues: 14.2892 Evaluate side-chains 111 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [39, 15, 19, 35, 23, 31, 25, 37, 42, 40, 0] chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.189130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.170393 restraints weight = 12245.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.176777 restraints weight = 6372.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.180876 restraints weight = 3616.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.183627 restraints weight = 2199.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.185361 restraints weight = 1387.214| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3668 Z= 0.170 Angle : 0.603 5.391 5008 Z= 0.324 Chirality : 0.053 0.386 571 Planarity : 0.005 0.047 638 Dihedral : 5.654 21.842 495 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.35 % Allowed : 16.97 % Favored : 80.68 % Cbeta Deviations : 0.23 % 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: -0.64 (0.38), residues: 455 helix: -0.83 (0.91), residues: 33 sheet: 1.21 (0.36), residues: 204 loop : -2.10 (0.36), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 104 TYR 0.009 0.001 TYR A 114 PHE 0.018 0.002 PHE A 87 TRP 0.009 0.002 TRP A 41 HIS 0.006 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 3668) covalent geometry : angle 0.60304 / 0.32 ( 5008) hydrogen bonds : bond 0.03393 / 2.26 ( 132) hydrogen bonds : angle 5.96122 / 4.18 ( 363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7414 (tpp-160) REVERT: A 117 SER cc_start: 0.9250 (m) cc_final: 0.9023 (m) REVERT: B 116 TYR cc_start: 0.8957 (p90) cc_final: 0.8585 (p90) REVERT: C 44 PHE cc_start: 0.7744 (t80) cc_final: 0.7494 (t80) REVERT: D 13 MET cc_start: 0.6670 (ttm) cc_final: 0.6008 (ttp) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.0947 time to fit residues: 13.9229 Evaluate side-chains 113 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 98 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [3, 2, 21, 4, 33, 36, 15, 7, 43, 24, 42] chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.191811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173193 restraints weight = 12254.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.179474 restraints weight = 6412.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.183578 restraints weight = 3657.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.186401 restraints weight = 2223.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.188201 restraints weight = 1377.539| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3668 Z= 0.121 Angle : 0.549 5.329 5008 Z= 0.293 Chirality : 0.051 0.374 571 Planarity : 0.004 0.036 638 Dihedral : 5.260 21.613 495 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.35 % Allowed : 18.02 % Favored : 79.63 % Cbeta Deviations : 0.23 % 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: -0.60 (0.39), residues: 455 helix: -0.51 (0.96), residues: 33 sheet: 1.17 (0.36), residues: 206 loop : -2.09 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 104 TYR 0.009 0.001 TYR A 114 PHE 0.013 0.002 PHE A 87 TRP 0.004 0.001 TRP A 41 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 3668) covalent geometry : angle 0.54873 / 0.29 ( 5008) hydrogen bonds : bond 0.03064 / 2.02 ( 132) hydrogen bonds : angle 5.70926 / 3.98 ( 363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7410 (tpp-160) REVERT: A 117 SER cc_start: 0.9239 (m) cc_final: 0.9006 (m) REVERT: B 116 TYR cc_start: 0.8952 (p90) cc_final: 0.8460 (p90) REVERT: C 80 LYS cc_start: 0.8211 (pttt) cc_final: 0.7662 (tptt) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 0.0992 time to fit residues: 14.3562 Evaluate side-chains 109 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [17, 5, 23, 38, 40, 32, 42, 20, 18, 25, 39] chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.189335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.171390 restraints weight = 12529.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.177475 restraints weight = 6554.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.181395 restraints weight = 3759.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.184044 restraints weight = 2301.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.185664 restraints weight = 1468.551| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3668 Z= 0.156 Angle : 0.566 5.584 5008 Z= 0.304 Chirality : 0.051 0.377 571 Planarity : 0.005 0.043 638 Dihedral : 5.381 21.267 495 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.09 % Allowed : 18.80 % Favored : 79.11 % Cbeta Deviations : 0.23 % 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: -0.73 (0.39), residues: 455 helix: -0.65 (0.94), residues: 33 sheet: 1.08 (0.37), residues: 206 loop : -2.16 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.009 0.001 TYR A 114 PHE 0.014 0.002 PHE A 87 TRP 0.006 0.001 TRP A 41 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 3668) covalent geometry : angle 0.56586 / 0.30 ( 5008) hydrogen bonds : bond 0.03080 / 2.06 ( 132) hydrogen bonds : angle 5.69993 / 3.98 ( 363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7424 (tpp-160) REVERT: A 117 SER cc_start: 0.9244 (m) cc_final: 0.9003 (m) REVERT: B 116 TYR cc_start: 0.8963 (p90) cc_final: 0.8616 (p90) REVERT: C 27 ASN cc_start: 0.5759 (OUTLIER) cc_final: 0.5526 (p0) REVERT: C 80 LYS cc_start: 0.8336 (pttt) cc_final: 0.7847 (tptt) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 0.0979 time to fit residues: 13.6627 Evaluate side-chains 110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 85 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [13, 38, 6, 36, 43, 39, 18, 15, 29, 40, 28] chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.189607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.172483 restraints weight = 12567.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.178262 restraints weight = 6581.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.182129 restraints weight = 3740.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.184482 restraints weight = 2280.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.186054 restraints weight = 1461.313| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3668 Z= 0.150 Angle : 0.560 5.611 5008 Z= 0.301 Chirality : 0.052 0.376 571 Planarity : 0.005 0.043 638 Dihedral : 5.404 20.879 495 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.87 % Allowed : 18.28 % Favored : 78.85 % Cbeta Deviations : 0.23 % 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: -0.69 (0.39), residues: 455 helix: 0.37 (1.03), residues: 27 sheet: 0.95 (0.37), residues: 212 loop : -2.17 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 34 TYR 0.009 0.001 TYR B 105 PHE 0.013 0.002 PHE A 87 TRP 0.007 0.001 TRP A 41 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 3668) covalent geometry : angle 0.55994 / 0.30 ( 5008) hydrogen bonds : bond 0.03032 / 2.00 ( 132) hydrogen bonds : angle 5.61358 / 3.93 ( 363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7538 (tpp-160) REVERT: B 13 MET cc_start: 0.6806 (ttm) cc_final: 0.6406 (ttt) REVERT: B 116 TYR cc_start: 0.8965 (p90) cc_final: 0.8675 (p90) REVERT: C 27 ASN cc_start: 0.5299 (OUTLIER) cc_final: 0.4755 (p0) REVERT: C 80 LYS cc_start: 0.8415 (pttt) cc_final: 0.7952 (tptt) outliers start: 11 outliers final: 9 residues processed: 106 average time/residue: 0.0963 time to fit residues: 13.4239 Evaluate side-chains 110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 85 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [30, 23, 5, 7, 24, 29, 33, 39, 2, 0, 26] chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.187059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.169070 restraints weight = 12664.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.175268 restraints weight = 6517.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.179200 restraints weight = 3666.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.181797 restraints weight = 2215.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.183489 restraints weight = 1396.441| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3668 Z= 0.158 Angle : 0.565 4.124 5008 Z= 0.307 Chirality : 0.051 0.375 571 Planarity : 0.005 0.044 638 Dihedral : 5.453 20.895 495 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.35 % Allowed : 18.54 % Favored : 79.11 % Cbeta Deviations : 0.23 % 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: -0.79 (0.39), residues: 455 helix: 0.29 (1.01), residues: 27 sheet: 0.89 (0.37), residues: 212 loop : -2.24 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.009 0.001 TYR A 114 PHE 0.015 0.002 PHE A 87 TRP 0.006 0.001 TRP C 41 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 3668) covalent geometry : angle 0.56517 / 0.31 ( 5008) hydrogen bonds : bond 0.03018 / 1.99 ( 132) hydrogen bonds : angle 5.64500 / 3.94 ( 363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7490 (tpp-160) REVERT: B 116 TYR cc_start: 0.8948 (p90) cc_final: 0.8599 (p90) REVERT: C 74 ASP cc_start: 0.8134 (m-30) cc_final: 0.7710 (p0) REVERT: C 80 LYS cc_start: 0.8451 (pttt) cc_final: 0.7964 (tptt) outliers start: 9 outliers final: 9 residues processed: 105 average time/residue: 0.0985 time to fit residues: 13.6534 Evaluate side-chains 109 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [12, 7, 32, 17, 43, 24, 5, 9, 0, 29, 38] chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.190971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.172731 restraints weight = 12603.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.179042 restraints weight = 6371.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.183087 restraints weight = 3543.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.185723 restraints weight = 2119.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.187297 restraints weight = 1333.995| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3668 Z= 0.110 Angle : 0.530 4.267 5008 Z= 0.282 Chirality : 0.051 0.365 571 Planarity : 0.005 0.039 638 Dihedral : 5.101 20.104 495 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.31 % Allowed : 20.37 % Favored : 78.33 % Cbeta Deviations : 0.23 % 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: -0.66 (0.40), residues: 455 helix: 0.69 (1.10), residues: 27 sheet: 0.74 (0.36), residues: 221 loop : -2.01 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.007 0.001 TYR B 105 PHE 0.012 0.002 PHE A 87 TRP 0.005 0.001 TRP C 41 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 3668) covalent geometry : angle 0.53009 / 0.28 ( 5008) hydrogen bonds : bond 0.02785 / 1.84 ( 132) hydrogen bonds : angle 5.47394 / 3.81 ( 363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7482 (tpp-160) REVERT: B 116 TYR cc_start: 0.8849 (p90) cc_final: 0.8582 (p90) REVERT: C 74 ASP cc_start: 0.8105 (m-30) cc_final: 0.7728 (p0) REVERT: C 80 LYS cc_start: 0.8391 (pttt) cc_final: 0.7992 (tptt) outliers start: 5 outliers final: 5 residues processed: 100 average time/residue: 0.1029 time to fit residues: 13.3126 Evaluate side-chains 102 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [18, 36, 6, 43, 3, 24, 30, 35, 41, 20, 14] chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.190199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.171443 restraints weight = 12687.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.177857 restraints weight = 6425.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.181893 restraints weight = 3571.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.184512 restraints weight = 2164.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.186259 restraints weight = 1389.567| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3668 Z= 0.106 Angle : 0.524 3.894 5008 Z= 0.278 Chirality : 0.051 0.367 571 Planarity : 0.005 0.039 638 Dihedral : 4.921 18.950 495 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.31 % Allowed : 20.63 % Favored : 78.07 % Cbeta Deviations : 0.23 % 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: -0.52 (0.40), residues: 455 helix: 0.86 (1.12), residues: 27 sheet: 0.84 (0.37), residues: 221 loop : -1.95 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.009 0.001 TYR B 105 PHE 0.011 0.001 PHE C 95 TRP 0.007 0.001 TRP C 41 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 3668) covalent geometry : angle 0.52412 / 0.28 ( 5008) hydrogen bonds : bond 0.02679 / 1.77 ( 132) hydrogen bonds : angle 5.35611 / 3.72 ( 363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7549 (tpp-160) REVERT: B 116 TYR cc_start: 0.8846 (p90) cc_final: 0.8568 (p90) REVERT: C 74 ASP cc_start: 0.8025 (m-30) cc_final: 0.7703 (p0) REVERT: C 80 LYS cc_start: 0.8399 (pttt) cc_final: 0.7998 (tptt) outliers start: 5 outliers final: 5 residues processed: 101 average time/residue: 0.1044 time to fit residues: 13.7549 Evaluate side-chains 101 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: [10, 41, 3, 14, 30, 23, 25, 5, 40, 31, 42] chunk 10 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.190697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.173568 restraints weight = 12646.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.179300 restraints weight = 6472.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.183213 restraints weight = 3641.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.185598 restraints weight = 2200.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.187128 restraints weight = 1399.467| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3668 Z= 0.122 Angle : 0.537 4.171 5008 Z= 0.288 Chirality : 0.051 0.370 571 Planarity : 0.005 0.040 638 Dihedral : 4.992 18.931 495 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.57 % Allowed : 20.89 % Favored : 77.55 % Cbeta Deviations : 0.23 % 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: -0.57 (0.40), residues: 455 helix: 0.86 (1.11), residues: 27 sheet: 0.84 (0.37), residues: 221 loop : -2.02 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.006 0.001 TYR A 114 PHE 0.012 0.002 PHE C 95 TRP 0.006 0.001 TRP A 41 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3668) covalent geometry : angle 0.53732 / 0.29 ( 5008) hydrogen bonds : bond 0.02765 / 1.85 ( 132) hydrogen bonds : angle 5.36213 / 3.72 ( 363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1699.06 seconds wall clock time: 29 minutes 34.71 seconds (1774.71 seconds total)