Starting phenix.real_space_refine on Wed Aug 5 01:11:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13kw_77126/08_2026/13kw_77126.cif Found real_map, /net/cci-nas-00/data/ceres_data/13kw_77126/08_2026/13kw_77126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13kw_77126/08_2026/13kw_77126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13kw_77126/08_2026/13kw_77126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13kw_77126/08_2026/13kw_77126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13kw_77126/08_2026/13kw_77126.map" } resolution = 4.0 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= 0.007 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: 4 Type Number sf(0) Gaussians C 2541 2.51 5 N 658 2.21 5 O 714 1.98 5 H 4046 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7959 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Restraints were copied for chains: B, C, D, E, F, G Residues with excluded nonbonded symmetry interactions: 294 residue: pdb=" N ALA A 5 " occ=0.00 ... (8 atoms not shown) pdb=" HB3 ALA A 5 " occ=0.00 residue: pdb=" N PHE A 6 " occ=0.00 ... (18 atoms not shown) pdb=" HZ PHE A 6 " occ=0.00 residue: pdb=" N ARG A 7 " occ=0.00 ... (22 atoms not shown) pdb="HH22 ARG A 7 " occ=0.00 residue: pdb=" N LYS A 8 " occ=0.00 ... (20 atoms not shown) pdb=" HZ3 LYS A 8 " occ=0.00 residue: pdb=" N LEU A 12 " occ=0.00 ... (17 atoms not shown) pdb="HD23 LEU A 12 " occ=0.00 residue: pdb=" N PHE A 13 " occ=0.00 ... (18 atoms not shown) pdb=" HZ PHE A 13 " occ=0.00 residue: pdb=" N ASP A 14 " occ=0.00 ... (10 atoms not shown) pdb=" HB3 ASP A 14 " occ=0.00 residue: pdb=" N GLY A 50 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY A 50 " occ=0.00 residue: pdb=" N SER A 51 " occ=0.00 ... (9 atoms not shown) pdb=" HG SER A 51 " occ=0.00 residue: pdb=" N GLY A 52 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY A 52 " occ=0.00 residue: pdb=" N SER A 53 " occ=0.00 ... (9 atoms not shown) pdb=" HG SER A 53 " occ=0.00 residue: pdb=" N LYS A 54 " occ=0.00 ... (20 atoms not shown) pdb=" HZ3 LYS A 54 " occ=0.00 ... (remaining 282 not shown) Time building chain proxies: 0.97, per 1000 atoms: 0.12 Number of scatterers: 7959 At special positions: 0 Unit cell: (93.07, 93.48, 48.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 714 8.00 N 658 7.00 C 2541 6.00 H 4046 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: 0.58 Conformation dependent library (CDL) restraints added in 298.3 milliseconds 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 882 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 83 Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 83 Processing sheet with id=AA3, first strand: chain 'C' and resid 79 through 83 Processing sheet with id=AA4, first strand: chain 'D' and resid 79 through 83 Processing sheet with id=AA5, first strand: chain 'E' and resid 79 through 83 Processing sheet with id=AA6, first strand: chain 'F' and resid 79 through 83 Processing sheet with id=AA7, first strand: chain 'G' and resid 79 through 83 42 hydrogen bonds defined for protein. 84 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: 1.22 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: 0.96 - 1.08: 1082 1.08 - 1.20: 2964 1.20 - 1.33: 805 1.33 - 1.45: 924 1.45 - 1.57: 2240 Bond restraints: 8015 Sorted by residual: bond pdb=" CZ ARG C 20 " pdb=" NH2 ARG C 20 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.30e-02 5.92e+03 5.88e+01 bond pdb=" CZ ARG B 20 " pdb=" NH2 ARG B 20 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.30e-02 5.92e+03 5.86e+01 bond pdb=" CZ ARG G 20 " pdb=" NH2 ARG G 20 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.83e+01 bond pdb=" CZ ARG A 20 " pdb=" NH2 ARG A 20 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.83e+01 bond pdb=" CZ ARG D 20 " pdb=" NH2 ARG D 20 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.82e+01 ... (remaining 8010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 10601 2.19 - 4.37: 2599 4.37 - 6.56: 910 6.56 - 8.75: 366 8.75 - 10.94: 91 Bond angle restraints: 14567 Sorted by residual: angle pdb=" N SER G 51 " pdb=" CA SER G 51 " pdb=" C SER G 51 " ideal model delta sigma weight residual 112.58 122.94 -10.36 1.22e+00 6.72e-01 7.21e+01 angle pdb=" N SER E 51 " pdb=" CA SER E 51 " pdb=" C SER E 51 " ideal model delta sigma weight residual 112.58 122.94 -10.36 1.22e+00 6.72e-01 7.20e+01 angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 112.58 122.93 -10.35 1.22e+00 6.72e-01 7.20e+01 angle pdb=" N SER B 51 " pdb=" CA SER B 51 " pdb=" C SER B 51 " ideal model delta sigma weight residual 112.58 122.93 -10.35 1.22e+00 6.72e-01 7.19e+01 angle pdb=" N SER C 51 " pdb=" CA SER C 51 " pdb=" C SER C 51 " ideal model delta sigma weight residual 112.58 122.92 -10.34 1.22e+00 6.72e-01 7.19e+01 ... (remaining 14562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 3045 14.76 - 29.51: 406 29.51 - 44.26: 84 44.26 - 59.02: 91 59.02 - 73.77: 56 Dihedral angle restraints: 3682 sinusoidal: 2058 harmonic: 1624 Sorted by residual: dihedral pdb=" CA PHE E 13 " pdb=" C PHE E 13 " pdb=" N ASP E 14 " pdb=" CA ASP E 14 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PHE D 13 " pdb=" C PHE D 13 " pdb=" N ASP D 14 " pdb=" CA ASP D 14 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PHE B 13 " pdb=" C PHE B 13 " pdb=" N ASP B 14 " pdb=" CA ASP B 14 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 3679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 485 0.144 - 0.289: 33 0.289 - 0.433: 49 0.433 - 0.577: 21 0.577 - 0.721: 14 Chirality restraints: 602 Sorted by residual: chirality pdb=" CB VAL E 82 " pdb=" CA VAL E 82 " pdb=" CG1 VAL E 82 " pdb=" CG2 VAL E 82 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CB VAL G 82 " pdb=" CA VAL G 82 " pdb=" CG1 VAL G 82 " pdb=" CG2 VAL G 82 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CB VAL F 82 " pdb=" CA VAL F 82 " pdb=" CG1 VAL F 82 " pdb=" CG2 VAL F 82 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 599 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 9 " 0.181 2.00e-02 2.50e+03 7.03e-02 1.48e+02 pdb=" CG PHE D 9 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 9 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE D 9 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 PHE D 9 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE D 9 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE D 9 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE D 9 " -0.057 2.00e-02 2.50e+03 pdb=" HD2 PHE D 9 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE D 9 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE D 9 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE D 9 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 9 " -0.181 2.00e-02 2.50e+03 7.03e-02 1.48e+02 pdb=" CG PHE G 9 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE G 9 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE G 9 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 PHE G 9 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE G 9 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE G 9 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE G 9 " 0.057 2.00e-02 2.50e+03 pdb=" HD2 PHE G 9 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE G 9 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE G 9 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE G 9 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 9 " -0.181 2.00e-02 2.50e+03 7.03e-02 1.48e+02 pdb=" CG PHE A 9 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 9 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE A 9 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 PHE A 9 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE A 9 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE A 9 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE A 9 " 0.057 2.00e-02 2.50e+03 pdb=" HD2 PHE A 9 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE A 9 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE A 9 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 9 " -0.100 2.00e-02 2.50e+03 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.52: 47 1.52 - 2.26: 1210 2.26 - 3.01: 21048 3.01 - 3.75: 28005 3.75 - 4.50: 43072 Warning: very small nonbonded interaction distances. Nonbonded interactions: 93382 Sorted by model distance: nonbonded pdb="HD23 LEU A 12 " pdb=" H LEU G 97 " model vdw 0.774 2.270 nonbonded pdb=" H LEU F 97 " pdb="HD23 LEU G 12 " model vdw 0.774 2.270 nonbonded pdb=" H LEU E 97 " pdb="HD23 LEU F 12 " model vdw 0.774 2.270 nonbonded pdb=" H LEU D 97 " pdb="HD23 LEU E 12 " model vdw 0.775 2.270 nonbonded pdb=" H LEU A 97 " pdb="HD23 LEU B 12 " model vdw 0.775 2.270 ... (remaining 93377 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=0.46 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: 3.670 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: 0.050 Extract box with map and model: 0.260 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.470 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1811 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.137 3969 Z= 1.228 Angle : 2.515 10.936 5320 Z= 1.565 Chirality : 0.193 0.721 602 Planarity : 0.016 0.086 679 Dihedral : 14.187 52.288 1477 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.09 % Favored : 73.91 % Rotamer: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Cbeta Deviations : 7.94 % 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: -4.02 (0.32), residues: 483 helix: None (None), residues: 0 sheet: -2.15 (0.49), residues: 84 loop : -3.10 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 15 TYR 0.042 0.018 TYR F 88 PHE 0.111 0.024 PHE D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.02197 / 1.23 ( 3969) covalent geometry : angle 2.51518 / 1.56 ( 5320) hydrogen bonds : bond 0.06462 / 3.88 ( 42) hydrogen bonds : angle 11.01026 / 7.26 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: -0.1700 (mp10) cc_final: -0.1908 (mp10) REVERT: B 61 GLN cc_start: -0.1417 (mp10) cc_final: -0.1724 (mp10) REVERT: C 59 GLU cc_start: 0.0588 (mm-30) cc_final: -0.0164 (mt-10) REVERT: C 89 PHE cc_start: 0.7067 (m-80) cc_final: 0.6823 (m-10) REVERT: D 59 GLU cc_start: 0.1334 (mm-30) cc_final: 0.1099 (mt-10) REVERT: D 61 GLN cc_start: -0.0879 (mp10) cc_final: -0.1188 (mp10) REVERT: D 89 PHE cc_start: 0.7076 (m-80) cc_final: 0.6843 (m-10) REVERT: E 61 GLN cc_start: -0.1207 (mp10) cc_final: -0.1457 (mp10) REVERT: F 61 GLN cc_start: -0.1582 (mp10) cc_final: -0.1908 (mp10) REVERT: G 61 GLN cc_start: -0.0088 (mp10) cc_final: -0.0820 (mp10) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1742 time to fit residues: 20.1785 Evaluate side-chains 76 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.5506 r_free = 0.5506 target = 0.353899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.327777 restraints weight = 15184.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5400 r_free = 0.5400 target = 0.337599 restraints weight = 5951.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5436 r_free = 0.5436 target = 0.343611 restraints weight = 2852.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5463 r_free = 0.5463 target = 0.347250 restraints weight = 1538.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5479 r_free = 0.5479 target = 0.349546 restraints weight = 887.318| |-----------------------------------------------------------------------------| r_work (final): 0.5498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2005 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 3969 Z= 0.299 Angle : 1.003 5.209 5320 Z= 0.548 Chirality : 0.059 0.171 602 Planarity : 0.006 0.039 679 Dihedral : 10.636 25.729 539 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 34.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.25 % Favored : 80.75 % Rotamer: Outliers : 1.69 % Allowed : 8.96 % Favored : 89.35 % 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: -4.58 (0.31), residues: 483 helix: None (None), residues: 0 sheet: -1.35 (0.41), residues: 154 loop : -4.24 (0.23), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 20 TYR 0.014 0.003 TYR A 88 PHE 0.015 0.003 PHE A 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.30 ( 3969) covalent geometry : angle 1.00290 / 0.55 ( 5320) hydrogen bonds : bond 0.03519 / 2.11 ( 42) hydrogen bonds : angle 12.41491 / 8.03 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.173 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: -0.2166 (mp10) cc_final: -0.2450 (mp10) REVERT: A 89 PHE cc_start: 0.6720 (m-80) cc_final: 0.6288 (m-10) REVERT: B 61 GLN cc_start: -0.2074 (mp10) cc_final: -0.2789 (mp10) REVERT: C 59 GLU cc_start: 0.0588 (mm-30) cc_final: 0.0310 (mt-10) REVERT: C 61 GLN cc_start: -0.1864 (mp10) cc_final: -0.2079 (mp10) REVERT: D 59 GLU cc_start: 0.2367 (mm-30) cc_final: 0.1818 (mt-10) REVERT: D 61 GLN cc_start: -0.1512 (mp10) cc_final: -0.1900 (mp10) REVERT: F 61 GLN cc_start: -0.2372 (mp10) cc_final: -0.2773 (mp10) REVERT: G 61 GLN cc_start: -0.1214 (mp10) cc_final: -0.1498 (mp10) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.1819 time to fit residues: 16.4324 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.5563 r_free = 0.5563 target = 0.360759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5369 r_free = 0.5369 target = 0.331757 restraints weight = 15225.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5435 r_free = 0.5435 target = 0.341934 restraints weight = 5963.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5480 r_free = 0.5480 target = 0.348435 restraints weight = 2955.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5507 r_free = 0.5507 target = 0.352527 restraints weight = 1656.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5527 r_free = 0.5527 target = 0.355196 restraints weight = 995.643| |-----------------------------------------------------------------------------| r_work (final): 0.5497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1914 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3969 Z= 0.150 Angle : 0.719 3.704 5320 Z= 0.390 Chirality : 0.049 0.132 602 Planarity : 0.003 0.016 679 Dihedral : 8.873 26.687 539 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.01 % Favored : 81.99 % Rotamer: Outliers : 0.48 % Allowed : 10.90 % Favored : 88.62 % 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: -4.35 (0.32), residues: 483 helix: None (None), residues: 0 sheet: -1.29 (0.41), residues: 154 loop : -4.01 (0.26), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 15 TYR 0.002 0.001 TYR D 76 PHE 0.015 0.002 PHE C 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.15 ( 3969) covalent geometry : angle 0.71942 / 0.39 ( 5320) hydrogen bonds : bond 0.01925 / 1.09 ( 42) hydrogen bonds : angle 10.11450 / 6.56 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.203 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 PHE cc_start: 0.6764 (m-80) cc_final: 0.6458 (m-10) REVERT: F 89 PHE cc_start: 0.6718 (m-80) cc_final: 0.6359 (m-10) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.1996 time to fit residues: 15.1747 Evaluate side-chains 59 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain C residue 86 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.5615 r_free = 0.5615 target = 0.360590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5330 r_free = 0.5330 target = 0.327204 restraints weight = 15041.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5406 r_free = 0.5406 target = 0.338409 restraints weight = 6828.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5468 r_free = 0.5468 target = 0.345955 restraints weight = 3630.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5501 r_free = 0.5501 target = 0.350697 restraints weight = 2082.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5524 r_free = 0.5524 target = 0.353810 restraints weight = 1272.422| |-----------------------------------------------------------------------------| r_work (final): 0.5504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1951 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3969 Z= 0.145 Angle : 0.706 3.795 5320 Z= 0.382 Chirality : 0.049 0.149 602 Planarity : 0.003 0.017 679 Dihedral : 8.419 25.309 539 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.98 % Favored : 83.02 % Rotamer: Outliers : 1.21 % Allowed : 8.23 % Favored : 90.56 % 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: -4.27 (0.33), residues: 483 helix: None (None), residues: 0 sheet: -1.18 (0.43), residues: 154 loop : -3.99 (0.26), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 15 TYR 0.004 0.001 TYR G 88 PHE 0.017 0.002 PHE G 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 3969) covalent geometry : angle 0.70645 / 0.38 ( 5320) hydrogen bonds : bond 0.02529 / 1.46 ( 42) hydrogen bonds : angle 10.10550 / 6.59 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.147 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 89 PHE cc_start: 0.6874 (m-80) cc_final: 0.6516 (m-10) REVERT: G 61 GLN cc_start: -0.0921 (mp10) cc_final: -0.1125 (mp10) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.1674 time to fit residues: 13.6117 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 71 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 7 optimal weight: 0.0970 chunk 2 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.5649 r_free = 0.5649 target = 0.363762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5357 r_free = 0.5357 target = 0.330054 restraints weight = 15005.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5434 r_free = 0.5434 target = 0.341007 restraints weight = 6849.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5495 r_free = 0.5495 target = 0.348619 restraints weight = 3707.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5529 r_free = 0.5529 target = 0.353457 restraints weight = 2158.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5553 r_free = 0.5553 target = 0.356708 restraints weight = 1335.896| |-----------------------------------------------------------------------------| r_work (final): 0.5515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1899 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3969 Z= 0.113 Angle : 0.648 3.732 5320 Z= 0.345 Chirality : 0.048 0.134 602 Planarity : 0.003 0.023 679 Dihedral : 7.939 25.107 539 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.70 % Favored : 79.30 % Rotamer: Outliers : 2.18 % Allowed : 11.38 % Favored : 86.44 % 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: -4.15 (0.34), residues: 483 helix: None (None), residues: 0 sheet: -1.30 (0.41), residues: 154 loop : -3.79 (0.29), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 15 TYR 0.005 0.000 TYR D 88 PHE 0.018 0.002 PHE A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.11 ( 3969) covalent geometry : angle 0.64847 / 0.35 ( 5320) hydrogen bonds : bond 0.02358 / 1.42 ( 42) hydrogen bonds : angle 9.62102 / 6.36 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.204 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: 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: symmetry clash REVERT: F 89 PHE cc_start: 0.6654 (m-80) cc_final: 0.6285 (m-10) outliers start: 9 outliers final: 9 residues processed: 91 average time/residue: 0.2231 time to fit residues: 22.9994 Evaluate side-chains 80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.0040 chunk 26 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.5932 r_free = 0.5932 target = 0.427485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5775 r_free = 0.5775 target = 0.419624 restraints weight = 192778.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5804 r_free = 0.5804 target = 0.422782 restraints weight = 112456.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5808 r_free = 0.5808 target = 0.423094 restraints weight = 93251.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5814 r_free = 0.5814 target = 0.423589 restraints weight = 89483.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5814 r_free = 0.5814 target = 0.423665 restraints weight = 86896.563| |-----------------------------------------------------------------------------| r_work (final): 0.5579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1908 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3969 Z= 0.101 Angle : 0.644 3.561 5320 Z= 0.338 Chirality : 0.048 0.128 602 Planarity : 0.005 0.043 679 Dihedral : 7.660 24.065 539 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.77 % Favored : 83.23 % Rotamer: Outliers : 3.15 % Allowed : 11.86 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.33), residues: 483 helix: None (None), residues: 0 sheet: -1.64 (0.38), residues: 154 loop : -3.78 (0.29), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 15 TYR 0.003 0.000 TYR D 88 PHE 0.008 0.001 PHE G 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 ( 3969) covalent geometry : angle 0.64440 / 0.34 ( 5320) hydrogen bonds : bond 0.02115 / 1.29 ( 42) hydrogen bonds : angle 8.36446 / 5.48 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLN cc_start: 0.3809 (mm-40) cc_final: 0.3492 (pt0) REVERT: F 89 PHE cc_start: 0.6451 (m-80) cc_final: 0.6120 (m-10) outliers start: 13 outliers final: 13 residues processed: 73 average time/residue: 0.2371 time to fit residues: 19.6128 Evaluate side-chains 75 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.5620 r_free = 0.5620 target = 0.359743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5354 r_free = 0.5354 target = 0.327880 restraints weight = 15388.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.338429 restraints weight = 6708.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5482 r_free = 0.5482 target = 0.345590 restraints weight = 3573.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5515 r_free = 0.5515 target = 0.350275 restraints weight = 2080.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.353263 restraints weight = 1279.810| |-----------------------------------------------------------------------------| r_work (final): 0.5512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2000 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3969 Z= 0.146 Angle : 0.711 3.747 5320 Z= 0.378 Chirality : 0.049 0.140 602 Planarity : 0.005 0.056 679 Dihedral : 7.770 23.598 539 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.77 % Favored : 83.23 % Rotamer: Outliers : 1.69 % Allowed : 11.62 % Favored : 86.68 % 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: -4.69 (0.32), residues: 483 helix: None (None), residues: 0 sheet: -1.90 (0.37), residues: 154 loop : -4.04 (0.28), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 15 TYR 0.004 0.001 TYR B 88 PHE 0.011 0.002 PHE A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 3969) covalent geometry : angle 0.71055 / 0.38 ( 5320) hydrogen bonds : bond 0.02886 / 1.66 ( 42) hydrogen bonds : angle 9.58138 / 6.23 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.206 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: 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: symmetry clash outliers start: 7 outliers final: 0 residues processed: 74 average time/residue: 0.1920 time to fit residues: 16.7025 Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.5627 r_free = 0.5627 target = 0.362099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5360 r_free = 0.5360 target = 0.331148 restraints weight = 15817.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5428 r_free = 0.5428 target = 0.341437 restraints weight = 6880.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5485 r_free = 0.5485 target = 0.348340 restraints weight = 3675.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5515 r_free = 0.5515 target = 0.352719 restraints weight = 2151.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5536 r_free = 0.5536 target = 0.355616 restraints weight = 1336.465| |-----------------------------------------------------------------------------| r_work (final): 0.5505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1991 moved from start: 0.9051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3969 Z= 0.152 Angle : 0.713 3.633 5320 Z= 0.379 Chirality : 0.049 0.133 602 Planarity : 0.005 0.036 679 Dihedral : 7.918 23.488 539 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.08 % Favored : 79.92 % Rotamer: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.31), residues: 483 helix: None (None), residues: 0 sheet: -2.06 (0.38), residues: 154 loop : -4.10 (0.26), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 15 TYR 0.005 0.001 TYR C 88 PHE 0.025 0.002 PHE C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3969) covalent geometry : angle 0.71318 / 0.38 ( 5320) hydrogen bonds : bond 0.02856 / 1.68 ( 42) hydrogen bonds : angle 10.32730 / 6.80 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 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: 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1967 time to fit residues: 14.4210 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.5654 r_free = 0.5654 target = 0.366264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5374 r_free = 0.5374 target = 0.333041 restraints weight = 15701.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5448 r_free = 0.5448 target = 0.344166 restraints weight = 6897.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5506 r_free = 0.5506 target = 0.351577 restraints weight = 3669.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5540 r_free = 0.5540 target = 0.356476 restraints weight = 2144.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5561 r_free = 0.5561 target = 0.359527 restraints weight = 1309.861| |-----------------------------------------------------------------------------| r_work (final): 0.5544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1910 moved from start: 0.9145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3969 Z= 0.101 Angle : 0.647 4.127 5320 Z= 0.337 Chirality : 0.048 0.129 602 Planarity : 0.005 0.036 679 Dihedral : 7.513 23.635 539 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.98 % Favored : 83.02 % Rotamer: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.33), residues: 483 helix: None (None), residues: 0 sheet: -2.01 (0.38), residues: 154 loop : -3.92 (0.28), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 15 TYR 0.003 0.000 TYR B 88 PHE 0.011 0.001 PHE C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 ( 3969) covalent geometry : angle 0.64681 / 0.34 ( 5320) hydrogen bonds : bond 0.02476 / 1.51 ( 42) hydrogen bonds : angle 9.22145 / 5.86 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 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: 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: F 89 PHE cc_start: 0.6279 (m-80) cc_final: 0.6025 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2069 time to fit residues: 13.3302 Evaluate side-chains 56 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 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 = 0.5649 r_free = 0.5649 target = 0.365297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5374 r_free = 0.5374 target = 0.333323 restraints weight = 15691.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5447 r_free = 0.5447 target = 0.343874 restraints weight = 6862.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5502 r_free = 0.5502 target = 0.351032 restraints weight = 3661.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5539 r_free = 0.5539 target = 0.355586 restraints weight = 2138.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.5560 r_free = 0.5560 target = 0.358559 restraints weight = 1318.900| |-----------------------------------------------------------------------------| r_work (final): 0.5524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1979 moved from start: 0.9350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3969 Z= 0.106 Angle : 0.650 3.919 5320 Z= 0.339 Chirality : 0.049 0.131 602 Planarity : 0.005 0.042 679 Dihedral : 7.360 22.677 539 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.01 % Favored : 81.99 % Rotamer: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.32), residues: 483 helix: None (None), residues: 0 sheet: -2.26 (0.37), residues: 154 loop : -3.92 (0.29), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 15 TYR 0.002 0.000 TYR C 76 PHE 0.013 0.002 PHE C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 3969) covalent geometry : angle 0.64993 / 0.34 ( 5320) hydrogen bonds : bond 0.02552 / 1.49 ( 42) hydrogen bonds : angle 8.55504 / 5.58 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.190 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: 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 outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1945 time to fit residues: 13.8639 Evaluate side-chains 60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.5610 r_free = 0.5610 target = 0.358820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5349 r_free = 0.5349 target = 0.327749 restraints weight = 16069.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5417 r_free = 0.5417 target = 0.338185 restraints weight = 6738.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5478 r_free = 0.5478 target = 0.345273 restraints weight = 3556.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5507 r_free = 0.5507 target = 0.349684 restraints weight = 2051.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5526 r_free = 0.5526 target = 0.352525 restraints weight = 1271.289| |-----------------------------------------------------------------------------| r_work (final): 0.5488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2053 moved from start: 0.9707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3969 Z= 0.161 Angle : 0.734 4.061 5320 Z= 0.387 Chirality : 0.050 0.137 602 Planarity : 0.006 0.047 679 Dihedral : 7.762 22.684 539 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 31.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.60 % Favored : 82.40 % Rotamer: Outliers : 0.97 % Allowed : 11.86 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.04 (0.32), residues: 483 helix: None (None), residues: 0 sheet: -2.46 (0.37), residues: 154 loop : -4.10 (0.28), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 15 TYR 0.006 0.001 TYR C 88 PHE 0.026 0.002 PHE B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 3969) covalent geometry : angle 0.73428 / 0.39 ( 5320) hydrogen bonds : bond 0.03281 / 1.87 ( 42) hydrogen bonds : angle 10.39328 / 6.71 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1524.08 seconds wall clock time: 26 minutes 17.03 seconds (1577.03 seconds total)