Starting phenix.real_space_refine on Thu Jul 2 01:30:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vzx_65487/07_2026/9vzx_65487_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vzx_65487/07_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_65487/07_2026/9vzx_65487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vzx_65487/07_2026/9vzx_65487.map" model { file = "/net/cci-nas-00/data/ceres_data/9vzx_65487/07_2026/9vzx_65487_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vzx_65487/07_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-dev-6108/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: 1.02, per 1000 atoms: 0.20 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: 0.31 Conformation dependent library (CDL) restraints added in 137.6 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: 0.38 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: 0.54 Time building geometry restraints manager: 0.44 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: 7173 1.20 - 2.40: 370 2.40 - 3.60: 98 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: 827 0.102 - 0.204: 37 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: 1.690 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.240 Find NCS groups from input model: 0.050 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- 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= 0.300 Angle : 0.681 6.002 7675 Z= 0.486 Chirality : 0.049 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 0.00408 / 0.30 ( 5462) covalent geometry : angle 0.68090 / 0.49 ( 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 : 0.167 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: 0.4203 time to fit residues: 28.5660 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 : 0.130 ------------------------------------------------------------------------------- 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: 9.9990 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: 20.0000 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... B 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.059813 restraints weight = 13597.805| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.88 r_work: 0.2854 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0944 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= 0.162 Angle : 0.628 11.657 7675 Z= 0.351 Chirality : 0.039 0.286 866 Planarity : 0.003 0.028 746 Dihedral : 21.987 155.140 1388 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.49 % Allowed : 17.71 % Favored : 79.80 % 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: 3.69 (0.37), residues: 477 helix: 3.23 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.64 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 103 TYR 0.016 0.002 TYR B 289 PHE 0.008 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 0.00319 / 0.16 ( 5462) covalent geometry : angle 0.62809 / 0.35 ( 7675) hydrogen bonds : bond 0.05059 / 3.32 ( 305) hydrogen bonds : angle 3.75142 / 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 72 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8919 (tp30) cc_final: 0.8523 (tm-30) REVERT: A 89 ASN cc_start: 0.9291 (t0) cc_final: 0.9067 (t0) REVERT: A 238 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8207 (mtt180) REVERT: B 170 SER cc_start: 0.9257 (m) cc_final: 0.8945 (p) REVERT: B 239 ASN cc_start: 0.8007 (t0) cc_final: 0.7712 (t0) outliers start: 10 outliers final: 1 residues processed: 67 average time/residue: 0.3715 time to fit residues: 26.1437 Evaluate side-chains 54 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU 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: 0.9980 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 0.0020 chunk 35 optimal weight: 0.0770 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0150 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.076999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.059778 restraints weight = 13662.526| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.92 r_work: 0.2855 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1227 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= 0.149 Angle : 0.565 8.084 7675 Z= 0.321 Chirality : 0.037 0.214 866 Planarity : 0.003 0.026 746 Dihedral : 22.064 154.741 1383 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.99 % Allowed : 16.71 % Favored : 80.30 % 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: 3.85 (0.38), residues: 477 helix: 3.32 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.79 (0.52), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.020 0.002 TYR B 289 PHE 0.009 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 0.00288 / 0.15 ( 5462) covalent geometry : angle 0.56518 / 0.32 ( 7675) hydrogen bonds : bond 0.04634 / 3.04 ( 305) hydrogen bonds : angle 3.63165 / 2.61 ( 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 70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.112 Fit side-chains REVERT: A 70 GLU cc_start: 0.8877 (tp30) cc_final: 0.8487 (tm-30) REVERT: A 89 ASN cc_start: 0.9327 (t0) cc_final: 0.9097 (t0) REVERT: A 127 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8706 (tp30) REVERT: A 238 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8224 (mtt180) REVERT: B 170 SER cc_start: 0.9216 (m) cc_final: 0.8910 (p) REVERT: B 223 GLN cc_start: 0.9010 (tt0) cc_final: 0.8310 (tm-30) REVERT: B 239 ASN cc_start: 0.8169 (t0) cc_final: 0.7791 (t0) outliers start: 12 outliers final: 4 residues processed: 67 average time/residue: 0.4110 time to fit residues: 28.8371 Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 247 CYS 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: 9.9990 chunk 50 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.076665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.059437 restraints weight = 13631.138| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.88 r_work: 0.2857 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5462 Z= 0.167 Angle : 0.545 6.531 7675 Z= 0.313 Chirality : 0.036 0.151 866 Planarity : 0.003 0.027 746 Dihedral : 22.103 165.550 1380 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 3.90 (0.38), residues: 477 helix: 3.36 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.81 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.020 0.002 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 B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 ( 5462) covalent geometry : angle 0.54487 / 0.31 ( 7675) hydrogen bonds : bond 0.04579 / 3.02 ( 305) hydrogen bonds : angle 3.62428 / 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 70 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9362 (tm) REVERT: A 70 GLU cc_start: 0.8910 (tp30) cc_final: 0.8489 (tm-30) REVERT: A 89 ASN cc_start: 0.9286 (t0) cc_final: 0.9039 (t0) REVERT: A 238 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8272 (mtt180) REVERT: B 170 SER cc_start: 0.9294 (m) cc_final: 0.8928 (p) REVERT: B 231 SER cc_start: 0.8225 (t) cc_final: 0.7155 (p) REVERT: B 239 ASN cc_start: 0.8138 (t0) cc_final: 0.7733 (t0) outliers start: 13 outliers final: 5 residues processed: 64 average time/residue: 0.3469 time to fit residues: 23.3977 Evaluate side-chains 59 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 208 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.077883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060641 restraints weight = 13819.572| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.93 r_work: 0.2876 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5462 Z= 0.132 Angle : 0.524 6.633 7675 Z= 0.299 Chirality : 0.036 0.149 866 Planarity : 0.003 0.026 746 Dihedral : 22.101 168.321 1380 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.49 % Allowed : 18.95 % Favored : 78.55 % 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: 3.84 (0.38), residues: 477 helix: 3.34 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.72 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.019 0.001 TYR B 289 PHE 0.010 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/Z covalent geometry : bond 0.00250 / 0.13 ( 5462) covalent geometry : angle 0.52367 / 0.30 ( 7675) hydrogen bonds : bond 0.04347 / 2.87 ( 305) hydrogen bonds : angle 3.53315 / 2.54 ( 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 66 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.147 Fit side-chains REVERT: A 70 GLU cc_start: 0.8902 (tp30) cc_final: 0.8491 (tm-30) REVERT: A 89 ASN cc_start: 0.9315 (t0) cc_final: 0.9047 (t0) REVERT: A 238 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8224 (mtt180) REVERT: A 239 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8510 (p0) REVERT: B 170 SER cc_start: 0.9281 (m) cc_final: 0.8930 (p) REVERT: B 231 SER cc_start: 0.8263 (t) cc_final: 0.7197 (p) REVERT: B 239 ASN cc_start: 0.8230 (t0) cc_final: 0.7829 (t0) outliers start: 10 outliers final: 3 residues processed: 62 average time/residue: 0.3242 time to fit residues: 21.2931 Evaluate side-chains 58 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET 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=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: 0.7980 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.076800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.059262 restraints weight = 13939.993| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.94 r_work: 0.2867 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1832 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= 0.167 Angle : 0.542 9.324 7675 Z= 0.306 Chirality : 0.036 0.146 866 Planarity : 0.003 0.028 746 Dihedral : 22.091 169.262 1380 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.75 % Allowed : 21.45 % 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: 3.73 (0.37), residues: 477 helix: 3.30 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.55 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 78 TYR 0.020 0.001 TYR B 289 PHE 0.009 0.001 PHE B 269 TRP 0.008 0.001 TRP B 67 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 ( 5462) covalent geometry : angle 0.54221 / 0.31 ( 7675) hydrogen bonds : bond 0.04447 / 2.95 ( 305) hydrogen bonds : angle 3.57750 / 2.57 ( 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 63 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.163 Fit side-chains REVERT: A 70 GLU cc_start: 0.8948 (tp30) cc_final: 0.8518 (tm-30) REVERT: A 89 ASN cc_start: 0.9293 (t0) cc_final: 0.9025 (t0) REVERT: A 238 ARG cc_start: 0.8616 (mtt180) cc_final: 0.8232 (mtt180) REVERT: A 239 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8539 (p0) REVERT: B 231 SER cc_start: 0.8157 (t) cc_final: 0.7052 (p) REVERT: B 239 ASN cc_start: 0.8232 (t0) cc_final: 0.7816 (t0) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 0.3501 time to fit residues: 21.8526 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 : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.074927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057606 restraints weight = 14009.160| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.91 r_work: 0.2829 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5462 Z= 0.237 Angle : 0.592 7.659 7675 Z= 0.330 Chirality : 0.038 0.152 866 Planarity : 0.004 0.032 746 Dihedral : 22.093 169.695 1380 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 3.63 (0.38), residues: 477 helix: 3.22 (0.27), residues: 325 sheet: None (None), residues: 0 loop : 0.58 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.024 0.002 TYR B 289 PHE 0.008 0.001 PHE B 269 TRP 0.009 0.001 TRP A 249 HIS 0.006 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 ( 5462) covalent geometry : angle 0.59160 / 0.33 ( 7675) hydrogen bonds : bond 0.04751 / 3.15 ( 305) hydrogen bonds : angle 3.66449 / 2.64 ( 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 60 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.103 Fit side-chains REVERT: A 70 GLU cc_start: 0.8962 (tp30) cc_final: 0.8518 (tm-30) REVERT: A 89 ASN cc_start: 0.9237 (t0) cc_final: 0.8960 (t0) REVERT: A 205 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8314 (tpt) REVERT: A 238 ARG cc_start: 0.8633 (mtt180) cc_final: 0.8231 (mtt180) REVERT: A 239 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8524 (p0) REVERT: B 170 SER cc_start: 0.9512 (m) cc_final: 0.8736 (p) REVERT: B 238 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8185 (mtt90) REVERT: B 239 ASN cc_start: 0.8262 (t0) cc_final: 0.7881 (t0) outliers start: 8 outliers final: 3 residues processed: 56 average time/residue: 0.3724 time to fit residues: 21.9077 Evaluate side-chains 56 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET 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 238 ARG Chi-restraints excluded: chain B residue 251 ASP 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: 0.7980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.076971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.060031 restraints weight = 13853.439| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.92 r_work: 0.2882 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5462 Z= 0.133 Angle : 0.533 7.991 7675 Z= 0.303 Chirality : 0.036 0.155 866 Planarity : 0.003 0.029 746 Dihedral : 22.074 170.710 1380 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.50 % Allowed : 21.70 % 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: 3.50 (0.38), residues: 477 helix: 3.08 (0.28), residues: 334 sheet: None (None), residues: 0 loop : 0.45 (0.49), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.018 0.001 TYR B 289 PHE 0.010 0.001 PHE B 269 TRP 0.006 0.001 TRP B 203 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 5462) covalent geometry : angle 0.53347 / 0.30 ( 7675) hydrogen bonds : bond 0.04323 / 2.88 ( 305) hydrogen bonds : angle 3.58180 / 2.59 ( 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 63 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.118 Fit side-chains REVERT: A 70 GLU cc_start: 0.8930 (tp30) cc_final: 0.8509 (tm-30) REVERT: A 89 ASN cc_start: 0.9235 (t0) cc_final: 0.8927 (t0) REVERT: A 144 MET cc_start: 0.9519 (OUTLIER) cc_final: 0.9238 (mmm) REVERT: A 238 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8265 (mtt180) REVERT: A 239 ASN cc_start: 0.9033 (OUTLIER) cc_final: 0.8577 (p0) REVERT: B 170 SER cc_start: 0.9452 (m) cc_final: 0.8715 (p) REVERT: B 223 GLN cc_start: 0.9013 (tt0) cc_final: 0.8278 (tm-30) REVERT: B 231 SER cc_start: 0.8137 (t) cc_final: 0.6996 (p) REVERT: B 238 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8198 (mtt90) REVERT: B 239 ASN cc_start: 0.8312 (t0) cc_final: 0.7922 (t0) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.3759 time to fit residues: 23.6605 Evaluate side-chains 58 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 238 ARG 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: 0.8980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.077386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.060339 restraints weight = 13850.194| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.95 r_work: 0.2886 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2221 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= 0.133 Angle : 0.542 9.573 7675 Z= 0.304 Chirality : 0.035 0.160 866 Planarity : 0.003 0.026 746 Dihedral : 22.010 171.764 1380 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.75 % Allowed : 22.44 % 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: 3.51 (0.37), residues: 477 helix: 3.08 (0.27), residues: 333 sheet: None (None), residues: 0 loop : 0.48 (0.49), 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 0.005 0.001 TRP A 274 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 5462) covalent geometry : angle 0.54155 / 0.30 ( 7675) hydrogen bonds : bond 0.04245 / 2.85 ( 305) hydrogen bonds : angle 3.59943 / 2.60 ( 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: 7 poor density : 55 time to evaluate : 0.102 Fit side-chains REVERT: A 70 GLU cc_start: 0.8930 (tp30) cc_final: 0.8511 (tm-30) REVERT: A 89 ASN cc_start: 0.9223 (t0) cc_final: 0.8924 (t0) REVERT: A 238 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8263 (mtt180) REVERT: A 239 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8555 (p0) REVERT: A 279 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8726 (mp0) REVERT: B 164 GLU cc_start: 0.8576 (mp0) cc_final: 0.8356 (pm20) REVERT: B 223 GLN cc_start: 0.8989 (tt0) cc_final: 0.8243 (tm-30) REVERT: B 231 SER cc_start: 0.8182 (t) cc_final: 0.7064 (p) REVERT: B 238 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8207 (mtt90) REVERT: B 239 ASN cc_start: 0.8336 (t0) cc_final: 0.7961 (t0) REVERT: B 251 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7827 (p0) outliers start: 7 outliers final: 1 residues processed: 59 average time/residue: 0.3845 time to fit residues: 23.7899 Evaluate side-chains 58 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain B residue 238 ARG 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: 8.9990 chunk 51 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.077338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060301 restraints weight = 13972.573| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.95 r_work: 0.2892 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2390 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= 0.140 Angle : 0.555 8.755 7675 Z= 0.310 Chirality : 0.036 0.197 866 Planarity : 0.003 0.024 746 Dihedral : 21.965 172.722 1380 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.25 % Allowed : 22.44 % 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: 3.43 (0.37), residues: 477 helix: 3.02 (0.27), residues: 333 sheet: None (None), residues: 0 loop : 0.48 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.016 0.001 TYR B 289 PHE 0.010 0.001 PHE B 269 TRP 0.005 0.001 TRP A 274 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 5462) covalent geometry : angle 0.55467 / 0.31 ( 7675) hydrogen bonds : bond 0.04213 / 2.81 ( 305) hydrogen bonds : angle 3.69056 / 2.68 ( 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 62 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.120 Fit side-chains REVERT: A 70 GLU cc_start: 0.8913 (tp30) cc_final: 0.8499 (tm-30) REVERT: A 89 ASN cc_start: 0.9231 (t0) cc_final: 0.8934 (t0) REVERT: A 238 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8261 (mtt180) REVERT: A 239 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8559 (p0) REVERT: A 279 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8733 (mp0) REVERT: B 86 MET cc_start: 0.9151 (mmm) cc_final: 0.8923 (mmm) REVERT: B 164 GLU cc_start: 0.8617 (mp0) cc_final: 0.8401 (pm20) REVERT: B 223 GLN cc_start: 0.8987 (tt0) cc_final: 0.8239 (tm-30) REVERT: B 238 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8215 (mtt90) REVERT: B 239 ASN cc_start: 0.8362 (t0) cc_final: 0.8004 (t0) REVERT: B 251 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7837 (p0) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.4161 time to fit residues: 26.5943 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 : 0.103 ------------------------------------------------------------------------------- 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 B residue 238 ARG 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: 5.9990 chunk 3 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.076214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.059302 restraints weight = 14045.592| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.91 r_work: 0.2861 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2336 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= 0.180 Angle : 0.561 9.393 7675 Z= 0.312 Chirality : 0.036 0.160 866 Planarity : 0.003 0.024 746 Dihedral : 21.944 173.835 1380 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 3.51 (0.37), residues: 477 helix: 3.08 (0.27), residues: 333 sheet: None (None), residues: 0 loop : 0.49 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 78 TYR 0.016 0.002 TYR B 289 PHE 0.009 0.001 PHE B 269 TRP 0.009 0.001 TRP A 249 HIS 0.007 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 5462) covalent geometry : angle 0.56060 / 0.31 ( 7675) hydrogen bonds : bond 0.04347 / 2.90 ( 305) hydrogen bonds : angle 3.63275 / 2.63 ( 857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1333.14 seconds wall clock time: 23 minutes 33.48 seconds (1413.48 seconds total)