Starting phenix.real_space_refine on Wed Jul 1 23:23:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kjr_22898/07_2026/7kjr_22898.map" } resolution = 2.08 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= 0.002 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 18 5.16 5 C 2446 2.51 5 N 580 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3840 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1575 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Time building chain proxies: 1.01, per 1000 atoms: 0.26 Number of scatterers: 3840 At special positions: 0 Unit cell: (77.789, 67.611, 90.148, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 2 15.00 O 794 8.00 N 580 7.00 C 2446 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: 0.22 Conformation dependent library (CDL) restraints added in 121.9 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 57.4% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.596A pdb=" N ILE A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 100 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.716A pdb=" N ILE B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 100 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 134 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'C' and resid 26 through 55 Proline residue: C 34 - end of helix removed outlier: 5.027A pdb=" N GLY C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 47 Proline residue: D 34 - end of helix Processing helix chain 'D' and resid 47 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160 removed outlier: 5.965A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU A 214 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN A 234 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 removed outlier: 5.963A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU B 214 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASN B 234 " --> pdb=" O LEU B 214 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 741 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: 0.56 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 857 1.33 - 1.45: 906 1.45 - 1.57: 2029 1.57 - 1.69: 2 1.69 - 1.81: 24 Bond restraints: 3818 Sorted by residual: bond pdb=" O4P PEE B 301 " pdb=" P PEE B 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" O4P PEE A 301 " pdb=" P PEE A 301 " ideal model delta sigma weight residual 1.653 1.769 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C4 PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 1.409 1.365 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C4 PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 1.409 1.366 0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C ILE B 62 " pdb=" O ILE B 62 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.19e-02 7.06e+03 2.25e+00 ... (remaining 3813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5035 1.99 - 3.98: 113 3.98 - 5.97: 27 5.97 - 7.96: 5 7.96 - 9.95: 6 Bond angle restraints: 5186 Sorted by residual: angle pdb=" CB GLN C 37 " pdb=" CG GLN C 37 " pdb=" CD GLN C 37 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.70e+00 3.46e-01 1.25e+01 angle pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " pdb=" CD GLU B 226 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O4P PEE A 301 " ideal model delta sigma weight residual 109.92 99.97 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O1P PEE B 301 " pdb=" P PEE B 301 " pdb=" O4P PEE B 301 " ideal model delta sigma weight residual 109.92 99.99 9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" O1P PEE A 301 " pdb=" P PEE A 301 " pdb=" O2P PEE A 301 " ideal model delta sigma weight residual 119.43 129.00 -9.57 3.00e+00 1.11e-01 1.02e+01 ... (remaining 5181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.49: 1993 20.49 - 40.98: 126 40.98 - 61.46: 42 61.46 - 81.95: 5 81.95 - 102.44: 4 Dihedral angle restraints: 2170 sinusoidal: 848 harmonic: 1322 Sorted by residual: dihedral pdb=" C32 PEE A 301 " pdb=" C30 PEE A 301 " pdb=" C31 PEE A 301 " pdb=" O3 PEE A 301 " ideal model delta sinusoidal sigma weight residual 161.16 -96.40 -102.44 1 3.00e+01 1.11e-03 1.30e+01 dihedral pdb=" CA HIS B 204 " pdb=" C HIS B 204 " pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA HIS A 204 " pdb=" C HIS A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 352 0.036 - 0.071: 156 0.071 - 0.107: 47 0.107 - 0.142: 15 0.142 - 0.178: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CG LEU B 147 " pdb=" CB LEU B 147 " pdb=" CD1 LEU B 147 " pdb=" CD2 LEU B 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 573 not shown) Planarity restraints: 626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 113 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C TYR B 113 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR B 113 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE B 114 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 37 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" CD GLN D 37 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN D 37 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN D 37 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 114 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C PHE B 114 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE B 114 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 115 " 0.011 2.00e-02 2.50e+03 ... (remaining 623 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 914 2.78 - 3.31: 3567 3.31 - 3.84: 7367 3.84 - 4.37: 8430 4.37 - 4.90: 13680 Nonbonded interactions: 33958 Sorted by model distance: nonbonded pdb=" O HOH A 424 " pdb=" O HOH A 451 " model vdw 2.254 3.040 nonbonded pdb=" O HOH B 401 " pdb=" O HOH B 433 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 216 " pdb=" OE1 GLN A 218 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 216 " pdb=" OE1 GLN B 218 " model vdw 2.276 3.040 nonbonded pdb=" O HOH A 401 " pdb=" O HOH A 437 " model vdw 2.294 3.040 ... (remaining 33953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.200 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.740 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:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 : 0.006 0.116 3818 Z= 0.288 Angle : 0.843 9.946 5186 Z= 0.426 Chirality : 0.047 0.178 576 Planarity : 0.005 0.036 626 Dihedral : 16.311 102.441 1322 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.25 % Allowed : 13.05 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.37), residues: 436 helix: 1.81 (0.31), residues: 234 sheet: 0.02 (0.48), residues: 90 loop : -0.81 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 29 TYR 0.011 0.002 TYR B 109 PHE 0.015 0.003 PHE B 146 TRP 0.013 0.002 TRP B 149 HIS 0.003 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.29 ( 3818) covalent geometry : angle 0.84253 / 0.43 ( 5186) hydrogen bonds : bond 0.10825 / 6.65 ( 253) hydrogen bonds : angle 5.94981 / 4.34 ( 741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.087 Fit side-chains REVERT: A 43 PHE cc_start: 0.7754 (m-10) cc_final: 0.6681 (t80) REVERT: A 136 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7714 (mmtm) REVERT: B 136 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7686 (mmtm) REVERT: B 192 LYS cc_start: 0.8741 (tttm) cc_final: 0.8044 (tptt) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.6311 time to fit residues: 44.7860 Evaluate side-chains 69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 ASN C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098351 restraints weight = 3700.129| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.60 r_work: 0.3050 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3818 Z= 0.135 Angle : 0.528 6.460 5186 Z= 0.284 Chirality : 0.041 0.131 576 Planarity : 0.003 0.034 626 Dihedral : 8.356 69.373 505 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.22 % Allowed : 11.58 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.37), residues: 436 helix: 2.90 (0.31), residues: 224 sheet: 0.14 (0.45), residues: 86 loop : -0.59 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.009 0.001 TYR B 109 PHE 0.011 0.002 PHE B 87 TRP 0.013 0.001 TRP A 149 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 3818) covalent geometry : angle 0.52804 / 0.28 ( 5186) hydrogen bonds : bond 0.04340 / 2.68 ( 253) hydrogen bonds : angle 4.62705 / 3.41 ( 741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.155 Fit side-chains REVERT: A 43 PHE cc_start: 0.7927 (m-10) cc_final: 0.6436 (t80) REVERT: A 136 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7696 (mmpt) REVERT: B 136 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7638 (mmpt) REVERT: B 152 ASN cc_start: 0.8265 (m-40) cc_final: 0.7123 (p0) REVERT: B 192 LYS cc_start: 0.8960 (tttm) cc_final: 0.8000 (tptt) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.5188 time to fit residues: 40.7679 Evaluate side-chains 76 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098110 restraints weight = 3583.696| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.57 r_work: 0.3042 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3818 Z= 0.148 Angle : 0.520 7.054 5186 Z= 0.280 Chirality : 0.041 0.130 576 Planarity : 0.003 0.035 626 Dihedral : 7.906 67.767 502 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.23 % Allowed : 12.32 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.38), residues: 436 helix: 3.15 (0.31), residues: 224 sheet: -0.23 (0.44), residues: 90 loop : -0.47 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.009 0.001 TYR B 109 PHE 0.012 0.002 PHE B 114 TRP 0.012 0.002 TRP A 149 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 3818) covalent geometry : angle 0.52039 / 0.28 ( 5186) hydrogen bonds : bond 0.04276 / 2.66 ( 253) hydrogen bonds : angle 4.56351 / 3.37 ( 741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.150 Fit side-chains REVERT: A 43 PHE cc_start: 0.7925 (m-10) cc_final: 0.6443 (t80) REVERT: A 68 ARG cc_start: 0.8260 (ttt-90) cc_final: 0.7840 (ttt90) REVERT: A 136 LYS cc_start: 0.8522 (mtpt) cc_final: 0.7686 (mmpt) REVERT: B 136 LYS cc_start: 0.8484 (mtpt) cc_final: 0.7657 (mmpt) REVERT: B 152 ASN cc_start: 0.8275 (m-40) cc_final: 0.7123 (p0) REVERT: B 192 LYS cc_start: 0.8961 (tttm) cc_final: 0.7991 (tptt) outliers start: 5 outliers final: 6 residues processed: 72 average time/residue: 0.5642 time to fit residues: 41.9519 Evaluate side-chains 76 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095791 restraints weight = 3613.031| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.61 r_work: 0.2986 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3818 Z= 0.156 Angle : 0.521 7.326 5186 Z= 0.279 Chirality : 0.041 0.129 576 Planarity : 0.003 0.036 626 Dihedral : 7.933 70.251 502 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 12.07 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.38), residues: 436 helix: 3.18 (0.32), residues: 224 sheet: -0.35 (0.45), residues: 90 loop : -0.46 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.010 0.001 TYR A 109 PHE 0.013 0.002 PHE A 87 TRP 0.011 0.002 TRP A 149 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 3818) covalent geometry : angle 0.52120 / 0.28 ( 5186) hydrogen bonds : bond 0.04261 / 2.66 ( 253) hydrogen bonds : angle 4.57151 / 3.38 ( 741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.152 Fit side-chains REVERT: A 43 PHE cc_start: 0.7866 (m-10) cc_final: 0.6272 (t80) REVERT: A 68 ARG cc_start: 0.8168 (ttt-90) cc_final: 0.7729 (ttt90) REVERT: A 136 LYS cc_start: 0.8404 (mtpt) cc_final: 0.7498 (mmpt) REVERT: B 136 LYS cc_start: 0.8382 (mtpt) cc_final: 0.7506 (mmpt) REVERT: B 152 ASN cc_start: 0.8235 (m-40) cc_final: 0.7004 (p0) REVERT: B 192 LYS cc_start: 0.8931 (tttm) cc_final: 0.7875 (tptt) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.5596 time to fit residues: 40.4183 Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096089 restraints weight = 3608.032| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.61 r_work: 0.2993 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3818 Z= 0.146 Angle : 0.510 7.147 5186 Z= 0.273 Chirality : 0.041 0.130 576 Planarity : 0.003 0.036 626 Dihedral : 7.849 71.842 502 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 12.32 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.38), residues: 436 helix: 3.20 (0.31), residues: 224 sheet: -0.39 (0.45), residues: 90 loop : -0.50 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.010 0.001 TYR A 109 PHE 0.012 0.002 PHE B 87 TRP 0.011 0.002 TRP A 149 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 3818) covalent geometry : angle 0.51027 / 0.27 ( 5186) hydrogen bonds : bond 0.04138 / 2.58 ( 253) hydrogen bonds : angle 4.52603 / 3.35 ( 741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.093 Fit side-chains REVERT: A 43 PHE cc_start: 0.7879 (m-10) cc_final: 0.6273 (t80) REVERT: A 68 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7719 (ttt90) REVERT: A 136 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7490 (mmpt) REVERT: B 136 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7498 (mmpt) REVERT: B 152 ASN cc_start: 0.8220 (m-40) cc_final: 0.7001 (p0) REVERT: B 192 LYS cc_start: 0.8924 (tttm) cc_final: 0.7875 (tptt) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.5644 time to fit residues: 41.2755 Evaluate side-chains 74 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096462 restraints weight = 3626.379| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.61 r_work: 0.2996 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3818 Z= 0.136 Angle : 0.500 6.849 5186 Z= 0.268 Chirality : 0.040 0.131 576 Planarity : 0.003 0.037 626 Dihedral : 7.747 73.643 502 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.99 % Allowed : 12.81 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.38), residues: 436 helix: 3.25 (0.31), residues: 224 sheet: -0.40 (0.44), residues: 90 loop : -0.52 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.009 0.001 TYR A 109 PHE 0.011 0.002 PHE B 87 TRP 0.012 0.002 TRP A 149 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 3818) covalent geometry : angle 0.50003 / 0.27 ( 5186) hydrogen bonds : bond 0.04018 / 2.50 ( 253) hydrogen bonds : angle 4.48047 / 3.32 ( 741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.089 Fit side-chains REVERT: A 43 PHE cc_start: 0.7867 (m-10) cc_final: 0.6249 (t80) REVERT: A 68 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7716 (ttt90) REVERT: A 136 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7493 (mmpt) REVERT: B 136 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7484 (mmpt) REVERT: B 152 ASN cc_start: 0.8237 (m-40) cc_final: 0.7013 (p0) REVERT: B 192 LYS cc_start: 0.8888 (tttm) cc_final: 0.7910 (tptt) outliers start: 4 outliers final: 5 residues processed: 70 average time/residue: 0.5607 time to fit residues: 40.4098 Evaluate side-chains 73 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096768 restraints weight = 3661.907| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.63 r_work: 0.3003 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3818 Z= 0.132 Angle : 0.499 6.705 5186 Z= 0.267 Chirality : 0.040 0.131 576 Planarity : 0.003 0.037 626 Dihedral : 7.642 75.403 502 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 13.05 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.38), residues: 436 helix: 3.27 (0.31), residues: 224 sheet: -0.41 (0.44), residues: 90 loop : -0.53 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.009 0.001 TYR A 109 PHE 0.010 0.002 PHE B 87 TRP 0.012 0.002 TRP A 149 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 3818) covalent geometry : angle 0.49880 / 0.27 ( 5186) hydrogen bonds : bond 0.03948 / 2.46 ( 253) hydrogen bonds : angle 4.45257 / 3.30 ( 741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.193 Fit side-chains REVERT: A 43 PHE cc_start: 0.7877 (m-10) cc_final: 0.6279 (t80) REVERT: A 68 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.7739 (ttt90) REVERT: A 136 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7487 (mmpt) REVERT: B 136 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7487 (mmpt) REVERT: B 152 ASN cc_start: 0.8227 (m-40) cc_final: 0.7009 (p0) REVERT: B 192 LYS cc_start: 0.8879 (tttm) cc_final: 0.7907 (tptt) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.5916 time to fit residues: 41.5151 Evaluate side-chains 69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 ASN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097487 restraints weight = 3639.102| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.61 r_work: 0.3014 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3818 Z= 0.122 Angle : 0.494 6.295 5186 Z= 0.263 Chirality : 0.040 0.131 576 Planarity : 0.003 0.037 626 Dihedral : 7.503 77.767 502 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 12.81 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.38), residues: 436 helix: 3.31 (0.31), residues: 224 sheet: -0.41 (0.44), residues: 90 loop : -0.54 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 29 TYR 0.008 0.001 TYR A 109 PHE 0.009 0.001 PHE B 87 TRP 0.017 0.002 TRP B 128 HIS 0.002 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 3818) covalent geometry : angle 0.49352 / 0.26 ( 5186) hydrogen bonds : bond 0.03820 / 2.38 ( 253) hydrogen bonds : angle 4.40821 / 3.27 ( 741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.168 Fit side-chains REVERT: A 43 PHE cc_start: 0.7916 (m-10) cc_final: 0.6298 (t80) REVERT: A 68 ARG cc_start: 0.8195 (ttt-90) cc_final: 0.7727 (ttt90) REVERT: A 136 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7473 (mmpt) REVERT: B 136 LYS cc_start: 0.8377 (mtpt) cc_final: 0.7480 (mmpt) REVERT: B 152 ASN cc_start: 0.8233 (m-40) cc_final: 0.7010 (p0) REVERT: B 192 LYS cc_start: 0.8856 (tttm) cc_final: 0.7900 (tptt) REVERT: C 36 THR cc_start: 0.7343 (m) cc_final: 0.7037 (p) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.5763 time to fit residues: 40.4263 Evaluate side-chains 70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 HIS C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096910 restraints weight = 3628.234| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.61 r_work: 0.3006 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3818 Z= 0.135 Angle : 0.512 6.778 5186 Z= 0.271 Chirality : 0.041 0.131 576 Planarity : 0.003 0.037 626 Dihedral : 7.590 79.311 502 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 12.81 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.38), residues: 436 helix: 3.28 (0.31), residues: 224 sheet: -0.39 (0.44), residues: 90 loop : -0.53 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.009 0.001 TYR B 109 PHE 0.011 0.002 PHE B 87 TRP 0.022 0.002 TRP B 128 HIS 0.003 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 3818) covalent geometry : angle 0.51201 / 0.27 ( 5186) hydrogen bonds : bond 0.03919 / 2.44 ( 253) hydrogen bonds : angle 4.46538 / 3.31 ( 741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.154 Fit side-chains REVERT: A 43 PHE cc_start: 0.7912 (m-10) cc_final: 0.6299 (t80) REVERT: A 68 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7728 (ttt90) REVERT: A 136 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7487 (mmpt) REVERT: B 136 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7503 (mmpt) REVERT: B 152 ASN cc_start: 0.8230 (m-40) cc_final: 0.7011 (p0) REVERT: B 192 LYS cc_start: 0.8873 (tttm) cc_final: 0.7910 (tptt) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.5482 time to fit residues: 38.4578 Evaluate side-chains 69 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 38 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 HIS C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096681 restraints weight = 3626.779| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.61 r_work: 0.3003 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3818 Z= 0.141 Angle : 0.527 6.938 5186 Z= 0.278 Chirality : 0.041 0.131 576 Planarity : 0.003 0.037 626 Dihedral : 7.670 80.487 502 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 13.05 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.38), residues: 436 helix: 3.26 (0.31), residues: 224 sheet: -0.38 (0.44), residues: 90 loop : -0.54 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 29 TYR 0.009 0.001 TYR A 109 PHE 0.011 0.002 PHE A 87 TRP 0.028 0.002 TRP B 128 HIS 0.003 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3818) covalent geometry : angle 0.52660 / 0.28 ( 5186) hydrogen bonds : bond 0.03977 / 2.48 ( 253) hydrogen bonds : angle 4.51067 / 3.34 ( 741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.147 Fit side-chains REVERT: A 43 PHE cc_start: 0.7906 (m-10) cc_final: 0.6283 (t80) REVERT: A 68 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7757 (ttt90) REVERT: A 136 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7498 (mmpt) REVERT: B 136 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7499 (mmpt) REVERT: B 152 ASN cc_start: 0.8234 (m-40) cc_final: 0.7015 (p0) REVERT: B 192 LYS cc_start: 0.8876 (tttm) cc_final: 0.7903 (tptt) outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.4880 time to fit residues: 34.2521 Evaluate side-chains 70 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain D residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 HIS C 42 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.100630 restraints weight = 3654.407| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.62 r_work: 0.3097 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3818 Z= 0.117 Angle : 0.503 5.990 5186 Z= 0.268 Chirality : 0.040 0.132 576 Planarity : 0.003 0.037 626 Dihedral : 7.494 83.788 502 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.23 % Allowed : 13.55 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.38), residues: 436 helix: 3.30 (0.31), residues: 224 sheet: -0.41 (0.44), residues: 90 loop : -0.54 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 68 TYR 0.008 0.001 TYR A 109 PHE 0.009 0.001 PHE B 87 TRP 0.032 0.002 TRP B 128 HIS 0.003 0.001 HIS B 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 3818) covalent geometry : angle 0.50328 / 0.27 ( 5186) hydrogen bonds : bond 0.03716 / 2.31 ( 253) hydrogen bonds : angle 4.40534 / 3.26 ( 741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2021.82 seconds wall clock time: 35 minutes 14.69 seconds (2114.69 seconds total)