Starting phenix.real_space_refine on Sat Apr 4 22:47:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vzx_65487/04_2026/9vzx_65487_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vzx_65487/04_2026/9vzx_65487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vzx_65487/04_2026/9vzx_65487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vzx_65487/04_2026/9vzx_65487.map" model { file = "/net/cci-nas-00/data/ceres_data/9vzx_65487/04_2026/9vzx_65487_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vzx_65487/04_2026/9vzx_65487_neut.cif" } resolution = 2.78 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= 0.024 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 65 5.49 5 S 24 5.16 5 C 3040 2.51 5 N 965 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5222 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1952 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 236} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1900 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 774 Classifications: {'DNA': 1, 'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 14, 'rna3p_pyr': 11} Link IDs: {'rna2p': 11, 'rna3p': 25} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 315 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 281 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Time building chain proxies: 1.34, per 1000 atoms: 0.26 Number of scatterers: 5222 At special positions: 0 Unit cell: (64.356, 64.356, 104.492, 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 24 16.00 P 65 15.00 O 1128 8.00 N 965 7.00 C 3040 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: 0.42 Conformation dependent library (CDL) restraints added in 235.8 milliseconds 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 71.6% alpha, 3.3% beta 16 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 65 through 99 removed outlier: 3.603A pdb=" N GLU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 removed outlier: 3.756A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 253 through 281 Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.777A pdb=" N ARG A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 99 removed outlier: 3.986A pdb=" N THR B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 135 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.818A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.097A pdb=" N TRP B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 195 through 210 Processing helix chain 'B' and resid 216 through 231 removed outlier: 4.062A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 301 through 306 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 238 263 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.56 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: 1315 1.33 - 1.45: 1346 1.45 - 1.57: 2629 1.57 - 1.69: 128 1.69 - 1.81: 44 Bond restraints: 5462 Sorted by residual: bond pdb=" P A C 37 " pdb=" OP2 A C 37 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" N ASP B 65 " pdb=" CA ASP B 65 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" P A C 37 " pdb=" OP1 A C 37 " ideal model delta sigma weight residual 1.480 1.515 -0.035 2.00e-02 2.50e+03 3.01e+00 bond pdb=" N ASP A 65 " pdb=" CA ASP A 65 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.75e+00 bond pdb=" P G C 36 " pdb=" OP1 G C 36 " ideal model delta sigma weight residual 1.485 1.516 -0.031 2.00e-02 2.50e+03 2.36e+00 ... (remaining 5457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 7269 1.20 - 2.40: 309 2.40 - 3.60: 65 3.60 - 4.80: 28 4.80 - 6.00: 4 Bond angle restraints: 7675 Sorted by residual: angle pdb=" N ILE B 178 " pdb=" CA ILE B 178 " pdb=" C ILE B 178 " ideal model delta sigma weight residual 111.77 108.49 3.28 1.04e+00 9.25e-01 9.93e+00 angle pdb=" C3' A C 17 " pdb=" O3' A C 17 " pdb=" P C C 18 " ideal model delta sigma weight residual 120.20 124.25 -4.05 1.50e+00 4.44e-01 7.28e+00 angle pdb=" N THR B 99 " pdb=" CA THR B 99 " pdb=" CB THR B 99 " ideal model delta sigma weight residual 113.65 109.73 3.92 1.47e+00 4.63e-01 7.10e+00 angle pdb=" C3' DT D 20 " pdb=" C2' DT D 20 " pdb=" C1' DT D 20 " ideal model delta sigma weight residual 101.60 105.53 -3.93 1.50e+00 4.44e-01 6.86e+00 angle pdb=" C3' DA D 14 " pdb=" C2' DA D 14 " pdb=" C1' DA D 14 " ideal model delta sigma weight residual 101.60 105.17 -3.57 1.50e+00 4.44e-01 5.65e+00 ... (remaining 7670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 2925 30.27 - 60.53: 266 60.53 - 90.79: 46 90.79 - 121.05: 2 121.05 - 151.32: 2 Dihedral angle restraints: 3241 sinusoidal: 1841 harmonic: 1400 Sorted by residual: dihedral pdb=" C4' DG D 18 " pdb=" C3' DG D 18 " pdb=" O3' DG D 18 " pdb=" P DA D 19 " ideal model delta sinusoidal sigma weight residual 220.00 68.68 151.32 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" C4' A C 17 " pdb=" C3' A C 17 " pdb=" O3' A C 17 " pdb=" P C C 18 " ideal model delta sinusoidal sigma weight residual 220.00 88.98 131.02 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" CA GLN B 98 " pdb=" C GLN B 98 " pdb=" N THR B 99 " pdb=" CA THR B 99 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 854 0.100 - 0.200: 10 0.200 - 0.300: 0 0.300 - 0.400: 0 0.400 - 0.501: 2 Chirality restraints: 866 Sorted by residual: chirality pdb=" P A C 37 " pdb=" OP1 A C 37 " pdb=" OP2 A C 37 " pdb=" O5' A C 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.85 -0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" P G C 36 " pdb=" OP1 G C 36 " pdb=" OP2 G C 36 " pdb=" O5' G C 36 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" C1' G C 2 " pdb=" O4' G C 2 " pdb=" C2' G C 2 " pdb=" N9 G C 2 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 863 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 103 " -0.194 9.50e-02 1.11e+02 8.77e-02 5.69e+00 pdb=" NE ARG B 103 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 103 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 103 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 103 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 190 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" CD GLU B 190 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 190 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 190 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 2 " 0.027 2.00e-02 2.50e+03 1.15e-02 3.97e+00 pdb=" N9 G C 2 " -0.027 2.00e-02 2.50e+03 pdb=" C8 G C 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C 2 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G C 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 2 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G C 2 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G C 2 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C 2 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 2 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G C 2 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G C 2 " -0.003 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 22 2.36 - 2.99: 2968 2.99 - 3.63: 8648 3.63 - 4.26: 13509 4.26 - 4.90: 20649 Nonbonded interactions: 45796 Sorted by model distance: nonbonded pdb=" O2' A C 17 " pdb=" OP1 C C 18 " model vdw 1.723 3.040 nonbonded pdb=" O2' C C 9 " pdb=" OP1 G C 10 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN B 239 " pdb=" N THR B 240 " model vdw 2.051 3.120 nonbonded pdb=" N GLN B 66 " pdb=" OE1 GLN B 66 " model vdw 2.086 3.120 nonbonded pdb=" N GLU B 308 " pdb=" OE1 GLU B 308 " model vdw 2.093 3.120 ... (remaining 45791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 290 or resid 298 through 309)) selection = (chain 'B' and (resid 65 through 135 or (resid 136 and (name N or name CA or nam \ e C or name O or name CB )) or resid 137 through 309)) } 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: 2.120 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:9.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5462 Z= 0.177 Angle : 0.634 6.002 7675 Z= 0.352 Chirality : 0.043 0.501 866 Planarity : 0.005 0.088 746 Dihedral : 20.596 151.317 2337 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.25 % Allowed : 24.69 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.37), residues: 477 helix: 3.31 (0.27), residues: 314 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 103 TYR 0.005 0.001 TYR A 217 PHE 0.008 0.001 PHE B 269 TRP 0.006 0.001 TRP B 67 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5462) covalent geometry : angle 0.63426 ( 7675) hydrogen bonds : bond 0.10654 ( 305) hydrogen bonds : angle 4.17125 ( 857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8911 (tp30) cc_final: 0.8543 (tm-30) REVERT: A 89 ASN cc_start: 0.9297 (t0) cc_final: 0.9080 (t0) REVERT: A 127 GLU cc_start: 0.8897 (tp30) cc_final: 0.8563 (OUTLIER) REVERT: A 133 LYS cc_start: 0.9566 (tppp) cc_final: 0.9199 (ttpp) REVERT: A 238 ARG cc_start: 0.8408 (mtt180) cc_final: 0.7994 (mtt180) REVERT: A 239 ASN cc_start: 0.8965 (t0) cc_final: 0.8545 (p0) outliers start: 5 outliers final: 6 residues processed: 65 average time/residue: 0.5694 time to fit residues: 38.5779 Evaluate side-chains 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 255 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.077557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060265 restraints weight = 13659.888| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.89 r_work: 0.2878 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5462 Z= 0.147 Angle : 0.564 6.602 7675 Z= 0.304 Chirality : 0.034 0.144 866 Planarity : 0.003 0.025 746 Dihedral : 22.155 169.596 1388 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.00 % Allowed : 18.95 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.37), residues: 477 helix: 3.53 (0.27), residues: 325 sheet: None (None), residues: 0 loop : 0.84 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 103 TYR 0.012 0.001 TYR A 160 PHE 0.009 0.001 PHE B 269 TRP 0.006 0.001 TRP B 67 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5462) covalent geometry : angle 0.56435 ( 7675) hydrogen bonds : bond 0.04266 ( 305) hydrogen bonds : angle 3.53697 ( 857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8950 (tp30) cc_final: 0.8537 (tm-30) REVERT: A 89 ASN cc_start: 0.9310 (t0) cc_final: 0.9086 (t0) REVERT: A 238 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8208 (mtt180) REVERT: B 223 GLN cc_start: 0.9022 (tt0) cc_final: 0.8302 (tm-30) REVERT: B 231 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7199 (p) REVERT: B 239 ASN cc_start: 0.8206 (t0) cc_final: 0.7881 (t0) outliers start: 8 outliers final: 2 residues processed: 71 average time/residue: 0.4909 time to fit residues: 36.5887 Evaluate side-chains 56 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.075373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057976 restraints weight = 13925.609| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.91 r_work: 0.2817 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5462 Z= 0.221 Angle : 0.581 7.238 7675 Z= 0.309 Chirality : 0.036 0.150 866 Planarity : 0.003 0.027 746 Dihedral : 22.199 171.504 1383 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.24 % Allowed : 19.70 % Favored : 78.05 % 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: 3.91 (0.37), residues: 477 helix: 3.40 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.74 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 103 TYR 0.016 0.002 TYR A 160 PHE 0.008 0.001 PHE B 269 TRP 0.007 0.001 TRP B 67 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5462) covalent geometry : angle 0.58074 ( 7675) hydrogen bonds : bond 0.04610 ( 305) hydrogen bonds : angle 3.57259 ( 857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.168 Fit side-chains REVERT: A 70 GLU cc_start: 0.8993 (tp30) cc_final: 0.8547 (tm-30) REVERT: A 89 ASN cc_start: 0.9316 (t0) cc_final: 0.9082 (t0) REVERT: A 238 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8166 (mtt180) REVERT: B 170 SER cc_start: 0.9537 (m) cc_final: 0.8814 (p) REVERT: B 239 ASN cc_start: 0.8336 (t0) cc_final: 0.7980 (t0) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.4604 time to fit residues: 29.4712 Evaluate side-chains 56 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 237 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.0970 chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.077282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060059 restraints weight = 13815.938| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.95 r_work: 0.2890 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5462 Z= 0.131 Angle : 0.522 6.299 7675 Z= 0.280 Chirality : 0.033 0.139 866 Planarity : 0.003 0.025 746 Dihedral : 22.081 174.282 1380 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.75 % Allowed : 21.95 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.37), residues: 477 helix: 3.52 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.89 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.012 0.001 TYR A 160 PHE 0.010 0.001 PHE B 269 TRP 0.006 0.001 TRP B 203 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5462) covalent geometry : angle 0.52176 ( 7675) hydrogen bonds : bond 0.03996 ( 305) hydrogen bonds : angle 3.42647 ( 857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.111 Fit side-chains REVERT: A 70 GLU cc_start: 0.8952 (tp30) cc_final: 0.8520 (tm-30) REVERT: A 89 ASN cc_start: 0.9303 (t0) cc_final: 0.9053 (t0) REVERT: A 238 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8155 (mtt180) REVERT: B 164 GLU cc_start: 0.8741 (mp0) cc_final: 0.8507 (pm20) REVERT: B 170 SER cc_start: 0.9456 (m) cc_final: 0.8941 (m) REVERT: B 239 ASN cc_start: 0.8320 (t0) cc_final: 0.7982 (t0) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 0.4881 time to fit residues: 30.6800 Evaluate side-chains 56 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 237 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057425 restraints weight = 14148.083| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.89 r_work: 0.2806 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5462 Z= 0.236 Angle : 0.585 7.126 7675 Z= 0.311 Chirality : 0.036 0.151 866 Planarity : 0.003 0.026 746 Dihedral : 22.149 173.889 1380 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.24 % Allowed : 20.45 % Favored : 76.31 % 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: 3.91 (0.37), residues: 477 helix: 3.46 (0.27), residues: 323 sheet: None (None), residues: 0 loop : 0.66 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 305 TYR 0.012 0.002 TYR B 289 PHE 0.008 0.001 PHE B 269 TRP 0.006 0.001 TRP B 67 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 5462) covalent geometry : angle 0.58458 ( 7675) hydrogen bonds : bond 0.04629 ( 305) hydrogen bonds : angle 3.61138 ( 857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.193 Fit side-chains REVERT: A 70 GLU cc_start: 0.9005 (tp30) cc_final: 0.8584 (tm-30) REVERT: A 89 ASN cc_start: 0.9318 (t0) cc_final: 0.9094 (t0) REVERT: A 164 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8986 (tp30) REVERT: A 238 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8152 (mtt180) REVERT: A 239 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8556 (p0) REVERT: B 170 SER cc_start: 0.9532 (m) cc_final: 0.9002 (m) REVERT: B 239 ASN cc_start: 0.8433 (t0) cc_final: 0.8104 (t0) REVERT: B 251 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8059 (p0) REVERT: B 299 ILE cc_start: 0.8588 (tp) cc_final: 0.8348 (tp) outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.4399 time to fit residues: 28.7734 Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 251 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 46 optimal weight: 0.0060 chunk 44 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 134 HIS B 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061376 restraints weight = 14028.027| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.98 r_work: 0.2912 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5462 Z= 0.125 Angle : 0.518 6.391 7675 Z= 0.278 Chirality : 0.033 0.141 866 Planarity : 0.003 0.026 746 Dihedral : 21.958 175.801 1380 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.24 % Allowed : 19.70 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.38), residues: 477 helix: 3.46 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.80 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.012 0.001 TYR B 289 PHE 0.010 0.001 PHE B 269 TRP 0.006 0.001 TRP A 274 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5462) covalent geometry : angle 0.51754 ( 7675) hydrogen bonds : bond 0.03923 ( 305) hydrogen bonds : angle 3.50629 ( 857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.106 Fit side-chains REVERT: A 70 GLU cc_start: 0.8973 (tp30) cc_final: 0.8553 (tm-30) REVERT: A 164 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8995 (tp30) REVERT: A 238 ARG cc_start: 0.8609 (mtt180) cc_final: 0.8180 (mtt180) REVERT: A 239 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8537 (p0) REVERT: A 279 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8711 (mp0) REVERT: B 164 GLU cc_start: 0.8760 (mp0) cc_final: 0.8560 (pm20) REVERT: B 170 SER cc_start: 0.9449 (m) cc_final: 0.8950 (m) REVERT: B 239 ASN cc_start: 0.8448 (t0) cc_final: 0.8123 (t0) REVERT: B 299 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8262 (tp) outliers start: 13 outliers final: 4 residues processed: 66 average time/residue: 0.4748 time to fit residues: 32.9073 Evaluate side-chains 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 134 HIS B 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.077740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.061079 restraints weight = 13959.319| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.92 r_work: 0.2902 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5462 Z= 0.133 Angle : 0.523 6.334 7675 Z= 0.281 Chirality : 0.033 0.138 866 Planarity : 0.003 0.031 746 Dihedral : 21.911 177.527 1380 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.24 % Allowed : 20.95 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.07 (0.37), residues: 477 helix: 3.55 (0.27), residues: 320 sheet: None (None), residues: 0 loop : 0.88 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 97 TYR 0.009 0.001 TYR B 289 PHE 0.009 0.001 PHE B 269 TRP 0.008 0.001 TRP B 67 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 5462) covalent geometry : angle 0.52333 ( 7675) hydrogen bonds : bond 0.03927 ( 305) hydrogen bonds : angle 3.48064 ( 857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.167 Fit side-chains REVERT: A 70 GLU cc_start: 0.8957 (tp30) cc_final: 0.8575 (tm-30) REVERT: A 164 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8990 (tp30) REVERT: A 238 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8162 (mtt180) REVERT: A 239 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8557 (p0) REVERT: A 279 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8710 (mp0) REVERT: B 86 MET cc_start: 0.9127 (mmm) cc_final: 0.8910 (mmm) REVERT: B 164 GLU cc_start: 0.8764 (mp0) cc_final: 0.8547 (pm20) REVERT: B 170 SER cc_start: 0.9446 (m) cc_final: 0.8929 (m) REVERT: B 239 ASN cc_start: 0.8488 (t0) cc_final: 0.8174 (t0) REVERT: B 299 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8292 (tp) outliers start: 9 outliers final: 3 residues processed: 61 average time/residue: 0.4641 time to fit residues: 29.6878 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058689 restraints weight = 14018.985| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.92 r_work: 0.2852 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5462 Z= 0.186 Angle : 0.551 7.856 7675 Z= 0.293 Chirality : 0.034 0.143 866 Planarity : 0.003 0.025 746 Dihedral : 21.902 178.739 1380 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.49 % Allowed : 21.70 % Favored : 75.81 % 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: 3.93 (0.37), residues: 477 helix: 3.43 (0.27), residues: 321 sheet: None (None), residues: 0 loop : 0.82 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.011 0.001 TYR A 160 PHE 0.007 0.001 PHE B 269 TRP 0.008 0.001 TRP B 67 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5462) covalent geometry : angle 0.55113 ( 7675) hydrogen bonds : bond 0.04275 ( 305) hydrogen bonds : angle 3.57314 ( 857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.9014 (tp30) cc_final: 0.8619 (tm-30) REVERT: A 164 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8876 (tp30) REVERT: A 238 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8217 (mtt-85) REVERT: A 239 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8586 (p0) REVERT: A 279 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8768 (mp0) REVERT: A 284 ASP cc_start: 0.9319 (m-30) cc_final: 0.9117 (t0) REVERT: B 164 GLU cc_start: 0.8787 (mp0) cc_final: 0.8554 (pm20) REVERT: B 239 ASN cc_start: 0.8474 (t0) cc_final: 0.8169 (t0) REVERT: B 299 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.4604 time to fit residues: 29.6056 Evaluate side-chains 61 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.078067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061394 restraints weight = 13925.016| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.92 r_work: 0.2910 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5462 Z= 0.135 Angle : 0.530 8.955 7675 Z= 0.281 Chirality : 0.033 0.137 866 Planarity : 0.003 0.031 746 Dihedral : 21.794 178.459 1380 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.25 % Allowed : 23.94 % Favored : 74.81 % 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: 3.97 (0.37), residues: 477 helix: 3.46 (0.27), residues: 320 sheet: None (None), residues: 0 loop : 0.88 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.013 0.001 TYR B 289 PHE 0.008 0.001 PHE B 269 TRP 0.006 0.001 TRP B 203 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5462) covalent geometry : angle 0.53004 ( 7675) hydrogen bonds : bond 0.03925 ( 305) hydrogen bonds : angle 3.57762 ( 857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.128 Fit side-chains REVERT: A 70 GLU cc_start: 0.8973 (tp30) cc_final: 0.8600 (tm-30) REVERT: A 164 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8953 (tp30) REVERT: A 238 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8178 (mtt180) REVERT: A 239 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8571 (p0) REVERT: A 279 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8756 (mp0) REVERT: B 164 GLU cc_start: 0.8801 (mp0) cc_final: 0.8550 (pm20) REVERT: B 170 SER cc_start: 0.9476 (m) cc_final: 0.8951 (m) REVERT: B 239 ASN cc_start: 0.8506 (t0) cc_final: 0.8230 (t0) REVERT: B 299 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8245 (tp) outliers start: 5 outliers final: 3 residues processed: 59 average time/residue: 0.4794 time to fit residues: 29.6569 Evaluate side-chains 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.0040 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.080379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.063803 restraints weight = 13931.394| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.96 r_work: 0.2972 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5462 Z= 0.120 Angle : 0.548 9.872 7675 Z= 0.289 Chirality : 0.033 0.141 866 Planarity : 0.004 0.053 746 Dihedral : 21.692 179.468 1380 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.25 % Allowed : 24.19 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.88 (0.37), residues: 477 helix: 3.36 (0.27), residues: 322 sheet: None (None), residues: 0 loop : 0.86 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.009 0.001 TYR B 289 PHE 0.008 0.001 PHE B 269 TRP 0.008 0.001 TRP B 203 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5462) covalent geometry : angle 0.54822 ( 7675) hydrogen bonds : bond 0.03778 ( 305) hydrogen bonds : angle 3.59402 ( 857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 954 Ramachandran restraints generated. 477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.182 Fit side-chains REVERT: A 70 GLU cc_start: 0.8929 (tp30) cc_final: 0.8562 (tm-30) REVERT: A 164 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8977 (tp30) REVERT: A 238 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8193 (mtt180) REVERT: A 239 ASN cc_start: 0.8994 (t0) cc_final: 0.8541 (p0) REVERT: A 279 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8716 (mp0) REVERT: B 164 GLU cc_start: 0.8807 (mp0) cc_final: 0.8567 (pm20) REVERT: B 170 SER cc_start: 0.9446 (m) cc_final: 0.8945 (m) REVERT: B 239 ASN cc_start: 0.8460 (t0) cc_final: 0.8221 (t0) outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.4671 time to fit residues: 32.4477 Evaluate side-chains 58 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 45 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.079336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062256 restraints weight = 14015.873| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.94 r_work: 0.2941 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5462 Z= 0.133 Angle : 0.560 9.726 7675 Z= 0.294 Chirality : 0.033 0.137 866 Planarity : 0.004 0.052 746 Dihedral : 21.624 178.433 1380 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.75 % Allowed : 24.69 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.37), residues: 477 helix: 3.46 (0.27), residues: 320 sheet: None (None), residues: 0 loop : 0.81 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.011 0.001 TYR B 289 PHE 0.006 0.001 PHE B 269 TRP 0.009 0.001 TRP B 203 HIS 0.006 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5462) covalent geometry : angle 0.55973 ( 7675) hydrogen bonds : bond 0.03851 ( 305) hydrogen bonds : angle 3.56994 ( 857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.12 seconds wall clock time: 29 minutes 57.38 seconds (1797.38 seconds total)