Starting phenix.real_space_refine on Tue Aug 4 17:11:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vzx_65487/08_2026/9vzx_65487_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vzx_65487/08_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_65487/08_2026/9vzx_65487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vzx_65487/08_2026/9vzx_65487.map" model { file = "/net/cci-nas-00/data/ceres_data/9vzx_65487/08_2026/9vzx_65487_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vzx_65487/08_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-2.2rc3-6140/lib/python3.11/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: 1.51, per 1000 atoms: 0.29 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: 0.37 Conformation dependent library (CDL) restraints added in 141.1 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: 0.64 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: 0.64 Time building geometry restraints manager: 0.51 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=" C1' DT D 20 " pdb=" N1 DT D 20 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.08e+00 bond pdb=" C1' DT E 29 " pdb=" N1 DT E 29 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.38e+00 bond pdb=" C3' DA D 14 " pdb=" C2' DA D 14 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.23e+00 bond pdb=" C1' DC E 30 " pdb=" N1 DC E 30 " ideal model delta sigma weight residual 1.468 1.498 -0.030 1.40e-02 5.10e+03 4.55e+00 bond pdb=" C1' DT E 25 " pdb=" N1 DT E 25 " ideal model delta sigma weight residual 1.468 1.497 -0.029 1.40e-02 5.10e+03 4.42e+00 ... (remaining 5457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 7071 1.20 - 2.40: 466 2.40 - 3.60: 104 3.60 - 4.80: 30 4.80 - 6.00: 4 Bond angle restraints: 7675 Sorted by residual: angle pdb=" N3 DT E 23 " pdb=" C4 DT E 23 " pdb=" O4 DT E 23 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT D 21 " pdb=" C4 DT D 21 " pdb=" O4 DT D 21 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT E 25 " pdb=" C4 DT E 25 " pdb=" O4 DT E 25 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" O4' DT E 25 " pdb=" C1' DT E 25 " pdb=" N1 DT E 25 " ideal model delta sigma weight residual 108.00 110.89 -2.89 7.00e-01 2.04e+00 1.70e+01 angle pdb=" N3 DT E 29 " pdb=" C4 DT E 29 " pdb=" O4 DT E 29 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (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 - 0.102: 819 0.102 - 0.204: 45 0.204 - 0.307: 0 0.307 - 0.409: 0 0.409 - 0.511: 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 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.52e+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=" C3' DC E 26 " pdb=" C4' DC E 26 " pdb=" O3' DC E 26 " pdb=" C2' DC E 26 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.17e-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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.830 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:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 0.040 5462 Z= 0.307 Angle : 0.717 6.002 7675 Z= 0.529 Chirality : 0.052 0.511 866 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/Z covalent geometry : bond 0.00413 / 0.31 ( 5462) covalent geometry : angle 0.71716 / 0.53 ( 7675) hydrogen bonds : bond 0.10654 / 6.74 ( 305) hydrogen bonds : angle 4.17125 / 3.04 ( 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 : 0.159 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: 0.5486 time to fit residues: 37.2416 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 : 0.181 ------------------------------------------------------------------------------- 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: 20.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.077101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059599 restraints weight = 13582.513| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.91 r_work: 0.2848 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5462 Z= 0.163 Angle : 0.638 11.389 7675 Z= 0.349 Chirality : 0.039 0.304 866 Planarity : 0.003 0.029 746 Dihedral : 21.900 154.251 1388 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.74 % Allowed : 17.71 % Favored : 79.55 % 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: 3.68 (0.37), residues: 477 helix: 3.22 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.65 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 103 TYR 0.015 0.002 TYR B 289 PHE 0.007 0.001 PHE B 269 TRP 0.006 0.001 TRP B 67 HIS 0.006 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 5462) covalent geometry : angle 0.63765 / 0.35 ( 7675) hydrogen bonds : bond 0.05021 / 3.29 ( 305) hydrogen bonds : angle 3.74998 / 2.71 ( 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 74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.195 Fit side-chains REVERT: A 70 GLU cc_start: 0.8926 (tp30) cc_final: 0.8535 (tm-30) REVERT: A 89 ASN cc_start: 0.9282 (t0) cc_final: 0.9059 (t0) REVERT: A 133 LYS cc_start: 0.9459 (tppp) cc_final: 0.9145 (tppt) REVERT: A 238 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8208 (mtt180) REVERT: B 239 ASN cc_start: 0.8009 (t0) cc_final: 0.7698 (t0) outliers start: 11 outliers final: 0 residues processed: 69 average time/residue: 0.5235 time to fit residues: 37.8603 Evaluate side-chains 54 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN B 204 ASN B 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.060412 restraints weight = 13672.781| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.92 r_work: 0.2883 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5462 Z= 0.134 Angle : 0.573 8.662 7675 Z= 0.319 Chirality : 0.037 0.248 866 Planarity : 0.003 0.026 746 Dihedral : 21.891 154.073 1380 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.24 % Allowed : 18.45 % Favored : 79.30 % 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: 3.86 (0.38), residues: 477 helix: 3.32 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.83 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 103 TYR 0.020 0.001 TYR B 289 PHE 0.010 0.001 PHE B 269 TRP 0.006 0.001 TRP B 67 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 5462) covalent geometry : angle 0.57335 / 0.32 ( 7675) hydrogen bonds : bond 0.04601 / 3.02 ( 305) hydrogen bonds : angle 3.63132 / 2.60 ( 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 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8888 (tp30) cc_final: 0.8484 (tm-30) REVERT: A 89 ASN cc_start: 0.9274 (t0) cc_final: 0.9052 (t0) REVERT: A 127 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8699 (tp30) REVERT: A 238 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8207 (mtt180) REVERT: B 223 GLN cc_start: 0.9016 (tt0) cc_final: 0.8300 (tm-30) REVERT: B 239 ASN cc_start: 0.8062 (t0) cc_final: 0.7685 (t0) outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.5287 time to fit residues: 35.3880 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 : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3414 r_free = 0.3414 target = 0.075856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058476 restraints weight = 13673.550| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.86 r_work: 0.2848 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5462 Z= 0.192 Angle : 0.567 6.889 7675 Z= 0.318 Chirality : 0.037 0.192 866 Planarity : 0.003 0.028 746 Dihedral : 21.938 162.269 1380 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.24 % Allowed : 17.96 % Favored : 78.80 % 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: 3.81 (0.38), residues: 477 helix: 3.29 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.78 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 305 TYR 0.018 0.001 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/Z covalent geometry : bond 0.00390 / 0.19 ( 5462) covalent geometry : angle 0.56749 / 0.32 ( 7675) hydrogen bonds : bond 0.04710 / 3.11 ( 305) hydrogen bonds : angle 3.61135 / 2.60 ( 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 69 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.163 Fit side-chains REVERT: A 68 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9352 (tm) REVERT: A 70 GLU cc_start: 0.8914 (tp30) cc_final: 0.8499 (tm-30) REVERT: A 89 ASN cc_start: 0.9296 (t0) cc_final: 0.9047 (t0) REVERT: A 238 ARG cc_start: 0.8588 (mtt180) cc_final: 0.8230 (mtt180) REVERT: B 231 SER cc_start: 0.8208 (t) cc_final: 0.7142 (p) REVERT: B 236 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8574 (tppt) REVERT: B 239 ASN cc_start: 0.8187 (t0) cc_final: 0.7791 (t0) outliers start: 13 outliers final: 3 residues processed: 64 average time/residue: 0.4580 time to fit residues: 30.8117 Evaluate side-chains 57 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3451 r_free = 0.3451 target = 0.077759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.060401 restraints weight = 13809.464| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.90 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: 0.8617 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5462 Z= 0.127 Angle : 0.526 6.843 7675 Z= 0.297 Chirality : 0.036 0.180 866 Planarity : 0.003 0.026 746 Dihedral : 21.949 163.442 1380 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.99 % Allowed : 19.70 % Favored : 77.31 % 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: 3.66 (0.38), residues: 477 helix: 3.17 (0.27), residues: 333 sheet: None (None), residues: 0 loop : 0.62 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.016 0.001 TYR B 289 PHE 0.011 0.001 PHE B 269 TRP 0.006 0.001 TRP B 67 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 ( 5462) covalent geometry : angle 0.52644 / 0.30 ( 7675) hydrogen bonds : bond 0.04395 / 2.89 ( 305) hydrogen bonds : angle 3.52329 / 2.53 ( 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 70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.249 Fit side-chains REVERT: A 70 GLU cc_start: 0.8906 (tp30) cc_final: 0.8493 (tm-30) REVERT: A 89 ASN cc_start: 0.9276 (t0) cc_final: 0.8995 (t0) REVERT: A 164 GLU cc_start: 0.9231 (tp30) cc_final: 0.9025 (mm-30) REVERT: A 238 ARG cc_start: 0.8590 (mtt180) cc_final: 0.8248 (mtt180) REVERT: B 223 GLN cc_start: 0.9033 (tt0) cc_final: 0.8292 (tm-30) REVERT: B 231 SER cc_start: 0.8269 (t) cc_final: 0.7215 (p) REVERT: B 236 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8584 (tppt) REVERT: B 239 ASN cc_start: 0.8190 (t0) cc_final: 0.7802 (t0) outliers start: 12 outliers final: 3 residues processed: 67 average time/residue: 0.4547 time to fit residues: 32.0811 Evaluate side-chains 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 299 ILE 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: 3.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.076941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.059912 restraints weight = 13891.176| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.89 r_work: 0.2886 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1922 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= 0.133 Angle : 0.535 9.614 7675 Z= 0.298 Chirality : 0.036 0.176 866 Planarity : 0.003 0.027 746 Dihedral : 21.898 164.967 1380 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.00 % Allowed : 21.70 % 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: 3.54 (0.37), residues: 477 helix: 3.13 (0.27), residues: 333 sheet: None (None), residues: 0 loop : 0.44 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 78 TYR 0.018 0.001 TYR B 289 PHE 0.010 0.001 PHE B 269 TRP 0.008 0.001 TRP B 67 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 5462) covalent geometry : angle 0.53454 / 0.30 ( 7675) hydrogen bonds : bond 0.04327 / 2.86 ( 305) hydrogen bonds : angle 3.55493 / 2.55 ( 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 68 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8901 (tp30) cc_final: 0.8482 (tm-30) REVERT: A 89 ASN cc_start: 0.9270 (t0) cc_final: 0.8997 (t0) REVERT: A 238 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8245 (mtt180) REVERT: A 279 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8700 (mp0) REVERT: B 223 GLN cc_start: 0.9032 (tt0) cc_final: 0.8275 (tm-30) REVERT: B 231 SER cc_start: 0.8242 (t) cc_final: 0.7171 (p) REVERT: B 236 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8592 (tppt) REVERT: B 239 ASN cc_start: 0.8219 (t0) cc_final: 0.7809 (t0) outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 0.5125 time to fit residues: 35.2958 Evaluate side-chains 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 251 ASP 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: 0.7980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.076676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.059489 restraints weight = 13851.524| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.87 r_work: 0.2870 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5462 Z= 0.156 Angle : 0.559 8.674 7675 Z= 0.309 Chirality : 0.036 0.173 866 Planarity : 0.003 0.025 746 Dihedral : 21.884 166.192 1380 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.74 % Allowed : 20.45 % 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: 3.43 (0.37), residues: 477 helix: 3.00 (0.27), residues: 334 sheet: None (None), residues: 0 loop : 0.49 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.021 0.002 TYR B 289 PHE 0.009 0.001 PHE B 269 TRP 0.008 0.001 TRP A 249 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 ( 5462) covalent geometry : angle 0.55895 / 0.31 ( 7675) hydrogen bonds : bond 0.04401 / 2.92 ( 305) hydrogen bonds : angle 3.58803 / 2.59 ( 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 69 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.166 Fit side-chains REVERT: A 70 GLU cc_start: 0.8914 (tp30) cc_final: 0.8490 (tm-30) REVERT: A 89 ASN cc_start: 0.9246 (t0) cc_final: 0.8951 (t0) REVERT: A 205 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8272 (tpt) REVERT: A 238 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8235 (mtt180) REVERT: A 239 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8461 (p0) REVERT: A 279 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8732 (mp0) REVERT: B 223 GLN cc_start: 0.9031 (tt0) cc_final: 0.8271 (tm-30) REVERT: B 231 SER cc_start: 0.8204 (t) cc_final: 0.7115 (p) REVERT: B 239 ASN cc_start: 0.8222 (t0) cc_final: 0.7822 (t0) outliers start: 11 outliers final: 3 residues processed: 65 average time/residue: 0.4941 time to fit residues: 33.5735 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 : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 251 ASP 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: 10.0000 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.077979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061013 restraints weight = 13809.861| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.91 r_work: 0.2903 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5462 Z= 0.130 Angle : 0.538 7.562 7675 Z= 0.301 Chirality : 0.036 0.159 866 Planarity : 0.003 0.026 746 Dihedral : 21.848 167.258 1380 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.25 % Allowed : 21.70 % 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: 3.41 (0.38), residues: 477 helix: 2.96 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.60 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 238 TYR 0.017 0.001 TYR B 289 PHE 0.009 0.001 PHE B 269 TRP 0.005 0.001 TRP B 67 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 5462) covalent geometry : angle 0.53831 / 0.30 ( 7675) hydrogen bonds : bond 0.04222 / 2.81 ( 305) hydrogen bonds : angle 3.60529 / 2.61 ( 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 66 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.183 Fit side-chains REVERT: A 70 GLU cc_start: 0.8920 (tp30) cc_final: 0.8505 (tm-30) REVERT: A 89 ASN cc_start: 0.9213 (t0) cc_final: 0.8897 (t0) REVERT: A 144 MET cc_start: 0.9518 (OUTLIER) cc_final: 0.9293 (mmm) REVERT: A 238 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8237 (mtt180) REVERT: A 239 ASN cc_start: 0.9000 (t0) cc_final: 0.8514 (p0) REVERT: A 279 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8710 (mp0) REVERT: B 223 GLN cc_start: 0.8989 (tt0) cc_final: 0.8259 (tm-30) REVERT: B 231 SER cc_start: 0.8158 (t) cc_final: 0.7052 (p) REVERT: B 239 ASN cc_start: 0.8250 (t0) cc_final: 0.7844 (t0) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 0.4615 time to fit residues: 30.9621 Evaluate side-chains 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 251 ASP 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: 0.9980 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.078066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061432 restraints weight = 13810.686| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.89 r_work: 0.2905 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5462 Z= 0.137 Angle : 0.560 9.623 7675 Z= 0.309 Chirality : 0.035 0.162 866 Planarity : 0.003 0.046 746 Dihedral : 21.794 168.252 1380 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 3.40 (0.37), residues: 477 helix: 2.98 (0.27), residues: 333 sheet: None (None), residues: 0 loop : 0.50 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 78 TYR 0.016 0.001 TYR B 289 PHE 0.009 0.001 PHE B 269 TRP 0.007 0.001 TRP A 249 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 5462) covalent geometry : angle 0.55988 / 0.31 ( 7675) hydrogen bonds : bond 0.04195 / 2.79 ( 305) hydrogen bonds : angle 3.61810 / 2.62 ( 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 67 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.099 Fit side-chains REVERT: A 70 GLU cc_start: 0.8917 (tp30) cc_final: 0.8500 (tm-30) REVERT: A 89 ASN cc_start: 0.9231 (t0) cc_final: 0.8918 (t0) REVERT: A 238 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8238 (mtt-85) REVERT: A 239 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8531 (p0) REVERT: A 279 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8690 (mp0) REVERT: B 223 GLN cc_start: 0.8991 (tt0) cc_final: 0.8252 (tm-30) REVERT: B 239 ASN cc_start: 0.8290 (t0) cc_final: 0.7914 (t0) REVERT: B 251 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7803 (p0) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.4221 time to fit residues: 28.2948 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 : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 251 ASP 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: 4.9990 chunk 51 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.078156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061567 restraints weight = 13933.728| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.90 r_work: 0.2908 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5462 Z= 0.141 Angle : 0.576 10.055 7675 Z= 0.313 Chirality : 0.036 0.170 866 Planarity : 0.003 0.041 746 Dihedral : 21.759 169.237 1380 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.50 % Allowed : 22.44 % Favored : 76.06 % 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: 3.39 (0.37), residues: 477 helix: 2.96 (0.27), residues: 333 sheet: None (None), residues: 0 loop : 0.53 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.015 0.001 TYR B 289 PHE 0.008 0.001 PHE B 269 TRP 0.008 0.001 TRP A 249 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 5462) covalent geometry : angle 0.57575 / 0.31 ( 7675) hydrogen bonds : bond 0.04185 / 2.79 ( 305) hydrogen bonds : angle 3.67980 / 2.67 ( 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 65 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.166 Fit side-chains REVERT: A 70 GLU cc_start: 0.8913 (tp30) cc_final: 0.8508 (tm-30) REVERT: A 89 ASN cc_start: 0.9240 (t0) cc_final: 0.8934 (t0) REVERT: A 144 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.9272 (mmm) REVERT: A 238 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8243 (mtt-85) REVERT: A 239 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8542 (p0) REVERT: A 279 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8701 (mp0) REVERT: B 223 GLN cc_start: 0.8995 (tt0) cc_final: 0.8247 (tm-30) REVERT: B 239 ASN cc_start: 0.8303 (t0) cc_final: 0.7936 (t0) REVERT: B 251 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7803 (p0) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.4032 time to fit residues: 26.4570 Evaluate side-chains 63 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 251 ASP 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 45 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.060264 restraints weight = 14082.935| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.95 r_work: 0.2883 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5462 Z= 0.158 Angle : 0.587 9.575 7675 Z= 0.318 Chirality : 0.036 0.164 866 Planarity : 0.003 0.037 746 Dihedral : 21.720 170.235 1380 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.00 % Allowed : 21.70 % 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: 3.53 (0.38), residues: 477 helix: 3.05 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.62 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.015 0.001 TYR B 289 PHE 0.008 0.001 PHE B 269 TRP 0.008 0.001 TRP A 249 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 5462) covalent geometry : angle 0.58745 / 0.32 ( 7675) hydrogen bonds : bond 0.04255 / 2.83 ( 305) hydrogen bonds : angle 3.59876 / 2.59 ( 857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1668.11 seconds wall clock time: 29 minutes 18.28 seconds (1758.28 seconds total)