Starting phenix.real_space_refine on Sat Aug 23 08:21:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl3_16711/08_2025/8cl3_16711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl3_16711/08_2025/8cl3_16711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cl3_16711/08_2025/8cl3_16711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl3_16711/08_2025/8cl3_16711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cl3_16711/08_2025/8cl3_16711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl3_16711/08_2025/8cl3_16711.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 774 atoms to isotropic. 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 S 72 5.16 5 C 6498 2.51 5 N 1770 2.21 5 O 1932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10272 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 1.66, per 1000 atoms: 0.16 Number of scatterers: 10272 At special positions: 0 Unit cell: (112.53, 112.53, 70.68, 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) S 72 16.00 O 1932 8.00 N 1770 7.00 C 6498 6.00 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: 1.04 Conformation dependent library (CDL) restraints added in 435.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 6 sheets defined 66.7% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 160 through 173 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 146 Processing helix chain 'I' and resid 160 through 173 Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 120 Processing helix chain 'K' and resid 125 through 146 Processing helix chain 'K' and resid 160 through 173 Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 Processing helix chain 'K' and resid 210 through 218 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'K' and resid 2 through 4 636 hydrogen bonds defined for protein. 1908 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: 1.65 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1752 1.32 - 1.44: 2538 1.44 - 1.56: 6078 1.56 - 1.68: 0 1.68 - 1.81: 132 Bond restraints: 10500 Sorted by residual: bond pdb=" C ARG G 143 " pdb=" O ARG G 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" C ARG A 143 " pdb=" O ARG A 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" C ARG I 143 " pdb=" O ARG I 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" C ARG C 143 " pdb=" O ARG C 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" C ARG E 143 " pdb=" O ARG E 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.22e+01 ... (remaining 10495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 13950 2.52 - 5.04: 294 5.04 - 7.56: 12 7.56 - 10.07: 12 10.07 - 12.59: 12 Bond angle restraints: 14280 Sorted by residual: angle pdb=" CB LEU E 6 " pdb=" CG LEU E 6 " pdb=" CD1 LEU E 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU K 6 " pdb=" CG LEU K 6 " pdb=" CD1 LEU K 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU C 6 " pdb=" CG LEU C 6 " pdb=" CD1 LEU C 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU I 6 " pdb=" CG LEU I 6 " pdb=" CD1 LEU I 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU A 6 " pdb=" CG LEU A 6 " pdb=" CD1 LEU A 6 " ideal model delta sigma weight residual 110.70 123.27 -12.57 3.00e+00 1.11e-01 1.76e+01 ... (remaining 14275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5874 17.20 - 34.39: 420 34.39 - 51.59: 72 51.59 - 68.79: 12 68.79 - 85.98: 6 Dihedral angle restraints: 6384 sinusoidal: 2532 harmonic: 3852 Sorted by residual: dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE I 32 " pdb=" C PHE I 32 " pdb=" N SER I 33 " pdb=" CA SER I 33 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE G 32 " pdb=" C PHE G 32 " pdb=" N SER G 33 " pdb=" CA SER G 33 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 1596 0.273 - 0.547: 0 0.547 - 0.820: 0 0.820 - 1.093: 0 1.093 - 1.367: 12 Chirality restraints: 1608 Sorted by residual: chirality pdb=" CG LEU K 6 " pdb=" CB LEU K 6 " pdb=" CD1 LEU K 6 " pdb=" CD2 LEU K 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" CG LEU E 6 " pdb=" CB LEU E 6 " pdb=" CD1 LEU E 6 " pdb=" CD2 LEU E 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" CG LEU G 6 " pdb=" CB LEU G 6 " pdb=" CD1 LEU G 6 " pdb=" CD2 LEU G 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.67e+01 ... (remaining 1605 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU A 136 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 137 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 136 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU G 136 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU G 136 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY G 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 136 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU E 136 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU E 136 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY E 137 " 0.016 2.00e-02 2.50e+03 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.77: 6 1.77 - 2.55: 36 2.55 - 3.33: 13324 3.33 - 4.12: 25712 4.12 - 4.90: 47520 Warning: very small nonbonded interaction distances. Nonbonded interactions: 86598 Sorted by model distance: nonbonded pdb=" CD2 LEU E 6 " pdb=" CA GLY G 8 " model vdw 0.985 3.860 nonbonded pdb=" CA GLY A 8 " pdb=" CD2 LEU K 6 " model vdw 0.985 3.860 nonbonded pdb=" CD2 LEU G 6 " pdb=" CA GLY I 8 " model vdw 0.985 3.860 nonbonded pdb=" CD2 LEU A 6 " pdb=" CA GLY C 8 " model vdw 0.985 3.860 nonbonded pdb=" CD2 LEU C 6 " pdb=" CA GLY E 8 " model vdw 0.985 3.860 ... (remaining 86593 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 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 : 0.005 0.068 10500 Z= 0.281 Angle : 0.974 12.594 14280 Z= 0.553 Chirality : 0.126 1.367 1608 Planarity : 0.009 0.056 1860 Dihedral : 12.731 85.982 3888 Min Nonbonded Distance : 0.985 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.21), residues: 1314 helix: -0.88 (0.15), residues: 870 sheet: None (None), residues: 0 loop : 0.20 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG K 167 TYR 0.027 0.008 TYR K 164 PHE 0.013 0.003 PHE B 9 TRP 0.018 0.003 TRP E 117 HIS 0.007 0.003 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00529 (10500) covalent geometry : angle 0.97355 (14280) hydrogen bonds : bond 0.12735 ( 636) hydrogen bonds : angle 6.48606 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.412 Fit side-chains REVERT: A 118 MET cc_start: 0.7654 (mtp) cc_final: 0.7411 (mtm) REVERT: C 143 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6837 (mtm-85) REVERT: E 118 MET cc_start: 0.7680 (mtp) cc_final: 0.7449 (mtp) REVERT: G 118 MET cc_start: 0.7651 (mtp) cc_final: 0.7409 (mtm) REVERT: K 118 MET cc_start: 0.7674 (mtp) cc_final: 0.7444 (mtp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1241 time to fit residues: 37.5779 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.1718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** 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 = 0.4251 r_free = 0.4251 target = 0.217194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.168299 restraints weight = 9251.809| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.83 r_work: 0.3485 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10500 Z= 0.119 Angle : 0.586 7.963 14280 Z= 0.284 Chirality : 0.043 0.142 1608 Planarity : 0.005 0.036 1860 Dihedral : 4.664 19.198 1410 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.02 % Allowed : 5.00 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.22), residues: 1314 helix: 0.88 (0.17), residues: 870 sheet: None (None), residues: 0 loop : 0.48 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 162 TYR 0.007 0.001 TYR E 169 PHE 0.007 0.001 PHE A 161 TRP 0.008 0.001 TRP I 117 HIS 0.003 0.001 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00265 (10500) covalent geometry : angle 0.58594 (14280) hydrogen bonds : bond 0.03979 ( 636) hydrogen bonds : angle 3.87147 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7147 (ttt) REVERT: C 212 GLU cc_start: 0.7182 (tt0) cc_final: 0.6952 (tp30) REVERT: E 35 GLU cc_start: 0.6957 (pm20) cc_final: 0.6725 (pm20) REVERT: E 55 MET cc_start: 0.7958 (mtm) cc_final: 0.7733 (mtp) REVERT: E 128 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: E 167 ARG cc_start: 0.7564 (mtp-110) cc_final: 0.7269 (ttp-110) REVERT: G 144 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7126 (ttt) REVERT: I 212 GLU cc_start: 0.7208 (tt0) cc_final: 0.6976 (tp30) REVERT: K 35 GLU cc_start: 0.6958 (pm20) cc_final: 0.6732 (pm20) REVERT: K 55 MET cc_start: 0.7975 (mtm) cc_final: 0.7755 (mtp) REVERT: K 128 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5870 (mp0) REVERT: K 167 ARG cc_start: 0.7561 (mtp-110) cc_final: 0.7263 (ttp-110) outliers start: 11 outliers final: 0 residues processed: 166 average time/residue: 0.1043 time to fit residues: 24.6431 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain K residue 128 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN D 7 GLN E 139 ASN F 7 GLN H 7 GLN J 7 GLN L 7 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.203043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.155172 restraints weight = 9431.679| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.65 r_work: 0.3379 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10500 Z= 0.183 Angle : 0.578 7.032 14280 Z= 0.286 Chirality : 0.044 0.143 1608 Planarity : 0.005 0.046 1860 Dihedral : 4.403 17.166 1410 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.39 % Allowed : 7.41 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.23), residues: 1314 helix: 0.97 (0.17), residues: 870 sheet: None (None), residues: 0 loop : 0.66 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.008 0.001 TYR C 130 PHE 0.009 0.002 PHE A 161 TRP 0.006 0.001 TRP E 80 HIS 0.002 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00458 (10500) covalent geometry : angle 0.57806 (14280) hydrogen bonds : bond 0.04250 ( 636) hydrogen bonds : angle 3.96509 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: C 128 GLU cc_start: 0.6302 (tp30) cc_final: 0.5957 (tp30) REVERT: E 128 GLU cc_start: 0.6124 (mp0) cc_final: 0.5730 (tm-30) REVERT: E 144 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7097 (ttm) REVERT: E 167 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.7202 (ttp-110) REVERT: I 128 GLU cc_start: 0.6322 (tp30) cc_final: 0.5976 (tp30) REVERT: K 128 GLU cc_start: 0.6127 (mp0) cc_final: 0.5722 (tm-30) REVERT: K 167 ARG cc_start: 0.7456 (mtp-110) cc_final: 0.7198 (ttp-110) outliers start: 15 outliers final: 9 residues processed: 152 average time/residue: 0.1079 time to fit residues: 23.1036 Evaluate side-chains 154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain K residue 15 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.210547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.162889 restraints weight = 9408.057| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.76 r_work: 0.3416 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10500 Z= 0.136 Angle : 0.518 7.034 14280 Z= 0.256 Chirality : 0.042 0.138 1608 Planarity : 0.005 0.050 1860 Dihedral : 4.069 14.875 1410 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.76 % Allowed : 6.94 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.23), residues: 1314 helix: 1.23 (0.18), residues: 870 sheet: -1.27 (0.53), residues: 54 loop : 0.42 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.007 0.001 TYR E 169 PHE 0.009 0.001 PHE C 32 TRP 0.003 0.001 TRP K 117 HIS 0.002 0.000 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00330 (10500) covalent geometry : angle 0.51808 (14280) hydrogen bonds : bond 0.03820 ( 636) hydrogen bonds : angle 3.78537 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.6859 (pm20) cc_final: 0.6634 (pm20) REVERT: A 144 MET cc_start: 0.7259 (ttm) cc_final: 0.6986 (ttt) REVERT: E 167 ARG cc_start: 0.7560 (mtp-110) cc_final: 0.7293 (ttp-110) REVERT: G 144 MET cc_start: 0.7236 (ttm) cc_final: 0.6983 (ttt) REVERT: G 212 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: K 167 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7310 (ttp-110) outliers start: 19 outliers final: 10 residues processed: 160 average time/residue: 0.1061 time to fit residues: 23.9230 Evaluate side-chains 164 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain K residue 146 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.200647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.152794 restraints weight = 9524.615| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.67 r_work: 0.3378 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 10500 Z= 0.189 Angle : 0.566 6.874 14280 Z= 0.282 Chirality : 0.044 0.141 1608 Planarity : 0.005 0.054 1860 Dihedral : 4.210 15.729 1410 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.59 % Allowed : 6.48 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.23), residues: 1314 helix: 1.19 (0.18), residues: 870 sheet: -1.20 (0.48), residues: 54 loop : 0.39 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.008 0.001 TYR K 169 PHE 0.008 0.001 PHE I 32 TRP 0.006 0.001 TRP E 80 HIS 0.002 0.001 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00471 (10500) covalent geometry : angle 0.56572 (14280) hydrogen bonds : bond 0.04185 ( 636) hydrogen bonds : angle 3.92638 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.496 Fit side-chains REVERT: A 75 GLU cc_start: 0.6069 (mt-10) cc_final: 0.5855 (mt-10) REVERT: A 212 GLU cc_start: 0.7798 (tp30) cc_final: 0.7538 (tp30) REVERT: C 128 GLU cc_start: 0.6134 (tp30) cc_final: 0.5712 (tp30) REVERT: E 128 GLU cc_start: 0.5873 (mp0) cc_final: 0.5592 (mp0) REVERT: E 144 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7097 (ttm) REVERT: E 167 ARG cc_start: 0.7459 (mtp-110) cc_final: 0.7212 (ttp-110) REVERT: G 212 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: I 128 GLU cc_start: 0.6166 (tp30) cc_final: 0.5714 (tp30) REVERT: K 118 MET cc_start: 0.7169 (mtm) cc_final: 0.6969 (mtp) REVERT: K 128 GLU cc_start: 0.5915 (mp0) cc_final: 0.5629 (mp0) REVERT: K 167 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7220 (ttp-110) outliers start: 28 outliers final: 16 residues processed: 161 average time/residue: 0.1088 time to fit residues: 24.8194 Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 146 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 87 optimal weight: 0.0020 chunk 95 optimal weight: 0.9980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.206976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.159972 restraints weight = 9599.457| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.70 r_work: 0.3458 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10500 Z= 0.114 Angle : 0.488 6.930 14280 Z= 0.240 Chirality : 0.040 0.135 1608 Planarity : 0.005 0.054 1860 Dihedral : 3.847 14.223 1410 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.02 % Allowed : 8.70 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.23), residues: 1314 helix: 1.47 (0.18), residues: 870 sheet: -1.00 (0.49), residues: 54 loop : 0.40 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 167 TYR 0.006 0.001 TYR E 169 PHE 0.009 0.001 PHE K 32 TRP 0.003 0.001 TRP G 23 HIS 0.001 0.000 HIS I 62 Details of bonding type rmsd covalent geometry : bond 0.00267 (10500) covalent geometry : angle 0.48836 (14280) hydrogen bonds : bond 0.03585 ( 636) hydrogen bonds : angle 3.71479 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 GLU cc_start: 0.6049 (tp30) cc_final: 0.5816 (tp30) REVERT: E 128 GLU cc_start: 0.5664 (mp0) cc_final: 0.5325 (mp0) REVERT: E 144 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6998 (ttm) REVERT: E 167 ARG cc_start: 0.7384 (mtp-110) cc_final: 0.7158 (ttp-110) REVERT: K 128 GLU cc_start: 0.5487 (mp0) cc_final: 0.5178 (mp0) REVERT: K 167 ARG cc_start: 0.7397 (mtp-110) cc_final: 0.7170 (ttp-110) outliers start: 11 outliers final: 9 residues processed: 152 average time/residue: 0.1136 time to fit residues: 24.3419 Evaluate side-chains 143 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain K residue 41 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.206241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.156516 restraints weight = 9539.721| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.87 r_work: 0.3344 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10500 Z= 0.186 Angle : 0.554 6.618 14280 Z= 0.275 Chirality : 0.043 0.139 1608 Planarity : 0.005 0.055 1860 Dihedral : 4.038 15.310 1410 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.31 % Allowed : 9.26 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.24), residues: 1314 helix: 1.30 (0.18), residues: 870 sheet: -1.13 (0.46), residues: 54 loop : 0.45 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.007 0.001 TYR E 169 PHE 0.008 0.001 PHE I 32 TRP 0.005 0.001 TRP A 80 HIS 0.002 0.001 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00464 (10500) covalent geometry : angle 0.55379 (14280) hydrogen bonds : bond 0.04068 ( 636) hydrogen bonds : angle 3.85713 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 GLU cc_start: 0.5906 (mp0) cc_final: 0.5594 (mp0) REVERT: E 144 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7026 (ttm) REVERT: E 167 ARG cc_start: 0.7365 (mtp-110) cc_final: 0.7141 (ttp-110) REVERT: G 35 GLU cc_start: 0.6806 (pm20) cc_final: 0.6601 (pm20) REVERT: G 212 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: K 118 MET cc_start: 0.7032 (mtm) cc_final: 0.6763 (mtp) REVERT: K 128 GLU cc_start: 0.5892 (mp0) cc_final: 0.5442 (mp0) REVERT: K 167 ARG cc_start: 0.7357 (mtp-110) cc_final: 0.7133 (ttp-110) outliers start: 25 outliers final: 21 residues processed: 154 average time/residue: 0.0865 time to fit residues: 18.8576 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain I residue 215 MET Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 146 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.0980 chunk 126 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 0.0030 chunk 86 optimal weight: 0.4980 chunk 113 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.212865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.167900 restraints weight = 9373.055| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.70 r_work: 0.3498 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10500 Z= 0.098 Angle : 0.468 6.499 14280 Z= 0.231 Chirality : 0.039 0.131 1608 Planarity : 0.005 0.053 1860 Dihedral : 3.638 14.252 1410 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.20 % Allowed : 10.00 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.23), residues: 1314 helix: 1.61 (0.18), residues: 876 sheet: -0.84 (0.47), residues: 54 loop : 0.53 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 167 TYR 0.004 0.001 TYR K 169 PHE 0.012 0.001 PHE K 32 TRP 0.004 0.001 TRP A 23 HIS 0.001 0.000 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00218 (10500) covalent geometry : angle 0.46809 (14280) hydrogen bonds : bond 0.03340 ( 636) hydrogen bonds : angle 3.64104 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.7164 (OUTLIER) cc_final: 0.6457 (m) REVERT: E 128 GLU cc_start: 0.5727 (mp0) cc_final: 0.5442 (mp0) REVERT: E 144 MET cc_start: 0.7364 (ttm) cc_final: 0.6997 (ttm) REVERT: E 167 ARG cc_start: 0.7506 (mtp-110) cc_final: 0.7278 (ttp-110) REVERT: G 41 SER cc_start: 0.7131 (OUTLIER) cc_final: 0.6400 (m) REVERT: K 118 MET cc_start: 0.7073 (mtm) cc_final: 0.6840 (mtp) REVERT: K 128 GLU cc_start: 0.5756 (mp0) cc_final: 0.5364 (mp0) REVERT: K 144 MET cc_start: 0.7563 (ttm) cc_final: 0.7347 (ttt) REVERT: K 167 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.7286 (ttp-110) outliers start: 13 outliers final: 7 residues processed: 152 average time/residue: 0.0823 time to fit residues: 17.7935 Evaluate side-chains 146 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 146 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.211083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.162176 restraints weight = 9401.597| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.85 r_work: 0.3381 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10500 Z= 0.151 Angle : 0.529 6.285 14280 Z= 0.263 Chirality : 0.042 0.147 1608 Planarity : 0.005 0.055 1860 Dihedral : 3.823 14.478 1410 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.93 % Allowed : 10.83 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1314 helix: 1.49 (0.18), residues: 876 sheet: -0.91 (0.46), residues: 54 loop : 0.59 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 167 TYR 0.007 0.001 TYR E 169 PHE 0.008 0.001 PHE I 32 TRP 0.005 0.001 TRP K 184 HIS 0.002 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00374 (10500) covalent geometry : angle 0.52874 (14280) hydrogen bonds : bond 0.03817 ( 636) hydrogen bonds : angle 3.81065 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 128 GLU cc_start: 0.5906 (tp30) cc_final: 0.5394 (mm-30) REVERT: E 128 GLU cc_start: 0.5758 (mp0) cc_final: 0.5302 (mp0) REVERT: E 144 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.7000 (ttm) REVERT: E 167 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.7142 (ttp-110) REVERT: I 128 GLU cc_start: 0.5921 (tp30) cc_final: 0.5402 (mm-30) REVERT: K 128 GLU cc_start: 0.5748 (mp0) cc_final: 0.5302 (mp0) REVERT: K 144 MET cc_start: 0.7519 (ttm) cc_final: 0.7275 (ttt) REVERT: K 167 ARG cc_start: 0.7374 (mtp-110) cc_final: 0.7164 (ttp-110) outliers start: 10 outliers final: 9 residues processed: 138 average time/residue: 0.0954 time to fit residues: 18.9788 Evaluate side-chains 143 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain K residue 39 MET Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 99 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.209835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.161130 restraints weight = 9366.250| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.84 r_work: 0.3397 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10500 Z= 0.134 Angle : 0.521 6.658 14280 Z= 0.258 Chirality : 0.041 0.135 1608 Planarity : 0.005 0.054 1860 Dihedral : 3.815 14.844 1410 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.02 % Allowed : 10.65 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1314 helix: 1.48 (0.18), residues: 876 sheet: -0.92 (0.45), residues: 54 loop : 0.61 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.006 0.001 TYR E 169 PHE 0.008 0.001 PHE I 32 TRP 0.005 0.001 TRP E 184 HIS 0.001 0.000 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00329 (10500) covalent geometry : angle 0.52103 (14280) hydrogen bonds : bond 0.03698 ( 636) hydrogen bonds : angle 3.81025 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 128 GLU cc_start: 0.5957 (tp30) cc_final: 0.5379 (mm-30) REVERT: E 118 MET cc_start: 0.7003 (mtm) cc_final: 0.6745 (mtp) REVERT: E 128 GLU cc_start: 0.5810 (mp0) cc_final: 0.5324 (mp0) REVERT: E 144 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6998 (ttm) REVERT: I 128 GLU cc_start: 0.5954 (tp30) cc_final: 0.5417 (mm-30) REVERT: K 118 MET cc_start: 0.6955 (mtm) cc_final: 0.6682 (mtp) REVERT: K 128 GLU cc_start: 0.5800 (mp0) cc_final: 0.5496 (mp0) REVERT: K 167 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.7167 (ttp-110) outliers start: 11 outliers final: 10 residues processed: 142 average time/residue: 0.0953 time to fit residues: 19.3113 Evaluate side-chains 147 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain I residue 41 SER Chi-restraints excluded: chain I residue 146 SER Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.204361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.156867 restraints weight = 9509.334| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.70 r_work: 0.3415 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10500 Z= 0.128 Angle : 0.511 6.333 14280 Z= 0.254 Chirality : 0.041 0.132 1608 Planarity : 0.005 0.054 1860 Dihedral : 3.768 14.383 1410 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.74 % Allowed : 11.02 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.24), residues: 1314 helix: 1.52 (0.18), residues: 876 sheet: -0.94 (0.45), residues: 54 loop : 0.64 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.006 0.001 TYR E 169 PHE 0.009 0.001 PHE K 32 TRP 0.016 0.001 TRP E 117 HIS 0.002 0.000 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00312 (10500) covalent geometry : angle 0.51112 (14280) hydrogen bonds : bond 0.03668 ( 636) hydrogen bonds : angle 3.81474 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.72 seconds wall clock time: 38 minutes 33.86 seconds (2313.86 seconds total)