Starting phenix.real_space_refine on Wed Jul 1 23:19:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9v_51158/07_2026/9g9v_51158.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9v_51158/07_2026/9g9v_51158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9v_51158/07_2026/9g9v_51158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9v_51158/07_2026/9g9v_51158.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9v_51158/07_2026/9g9v_51158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9v_51158/07_2026/9g9v_51158.cif" } resolution = 3.32 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= 0.032 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 K 5 8.98 5 S 32 5.16 5 C 2692 2.51 5 N 652 2.21 5 O 692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 4073 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1964 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 256} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1964 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 4, 'TRANS': 256} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Ad-hoc single atom residues: {' K': 5} Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.12, per 1000 atoms: 0.27 Number of scatterers: 4073 At special positions: 0 Unit cell: (62.4, 79.04, 96.512, 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) K 5 19.00 S 32 16.00 O 692 8.00 N 652 7.00 C 2692 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: 0.38 Conformation dependent library (CDL) restraints added in 153.7 milliseconds 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 86.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 1 through 52 removed outlier: 4.361A pdb=" N ASN A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 39 " --> pdb=" O MET A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 Proline residue: A 71 - end of helix removed outlier: 4.169A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.667A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 removed outlier: 3.813A pdb=" N GLN A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 removed outlier: 3.569A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.881A pdb=" N LEU A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 52 removed outlier: 3.563A pdb=" N VAL B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 39 " --> pdb=" O MET B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 Proline residue: B 71 - end of helix removed outlier: 4.169A pdb=" N ALA B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 removed outlier: 3.667A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 removed outlier: 3.813A pdb=" N GLN B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 removed outlier: 3.569A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.881A pdb=" N LEU B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN B 250 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.40 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 622 1.32 - 1.44: 1160 1.44 - 1.56: 2336 1.56 - 1.68: 0 1.68 - 1.80: 50 Bond restraints: 4168 Sorted by residual: bond pdb=" CG1 ILE B 118 " pdb=" CD1 ILE B 118 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.20e+00 bond pdb=" CG1 ILE A 118 " pdb=" CD1 ILE A 118 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.20e+00 bond pdb=" CB THR A 198 " pdb=" CG2 THR A 198 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CB THR B 198 " pdb=" CG2 THR B 198 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CG1 ILE B 94 " pdb=" CD1 ILE B 94 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.52e+00 ... (remaining 4163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 5073 1.10 - 2.20: 499 2.20 - 3.30: 62 3.30 - 4.40: 28 4.40 - 5.50: 12 Bond angle restraints: 5674 Sorted by residual: angle pdb=" C LEU A 29 " pdb=" N GLU A 30 " pdb=" CA GLU A 30 " ideal model delta sigma weight residual 120.23 115.27 4.96 1.67e+00 3.59e-01 8.84e+00 angle pdb=" C LEU B 29 " pdb=" N GLU B 30 " pdb=" CA GLU B 30 " ideal model delta sigma weight residual 120.23 115.27 4.96 1.67e+00 3.59e-01 8.84e+00 angle pdb=" N GLU B 30 " pdb=" CA GLU B 30 " pdb=" C GLU B 30 " ideal model delta sigma weight residual 112.99 117.64 -4.65 1.61e+00 3.86e-01 8.35e+00 angle pdb=" N GLU A 30 " pdb=" CA GLU A 30 " pdb=" C GLU A 30 " ideal model delta sigma weight residual 112.99 117.64 -4.65 1.61e+00 3.86e-01 8.35e+00 angle pdb=" CA GLN B 209 " pdb=" C GLN B 209 " pdb=" N THR B 210 " ideal model delta sigma weight residual 114.76 117.65 -2.89 1.14e+00 7.69e-01 6.41e+00 ... (remaining 5669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 2416 15.06 - 30.12: 134 30.12 - 45.18: 36 45.18 - 60.24: 12 60.24 - 75.30: 4 Dihedral angle restraints: 2602 sinusoidal: 1088 harmonic: 1514 Sorted by residual: dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LYS A 79 " pdb=" C LYS A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual 180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL B 243 " pdb=" C VAL B 243 " pdb=" N LEU B 244 " pdb=" CA LEU B 244 " ideal model delta harmonic sigma weight residual 180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2599 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 356 0.037 - 0.073: 205 0.073 - 0.109: 85 0.109 - 0.145: 10 0.145 - 0.181: 8 Chirality restraints: 664 Sorted by residual: chirality pdb=" CA GLU A 30 " pdb=" N GLU A 30 " pdb=" C GLU A 30 " pdb=" CB GLU A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU B 30 " pdb=" N GLU B 30 " pdb=" C GLU B 30 " pdb=" CB GLU B 30 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 661 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 24 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA B 24 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA B 24 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 25 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 24 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C ALA A 24 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 24 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 85 " 0.010 2.00e-02 2.50e+03 1.43e-02 4.07e+00 pdb=" CG TYR A 85 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 85 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 85 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 85 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 85 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 85 " 0.021 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.82: 1118 2.82 - 3.40: 4864 3.40 - 3.98: 7465 3.98 - 4.56: 10505 4.56 - 5.14: 15075 Nonbonded interactions: 39027 Sorted by model distance: nonbonded pdb=" OD1 ASP A 27 " pdb=" OG SER B 83 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 83 " pdb=" OD1 ASP B 27 " model vdw 2.245 3.040 nonbonded pdb=" O THR B 198 " pdb=" OG1 THR B 199 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 92 " pdb=" OG1 THR A 93 " model vdw 2.445 3.040 ... (remaining 39022 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 1 through 302) selection = chain 'B' } 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.350 Find NCS groups from input model: 0.040 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.007 0.070 4168 Z= 0.299 Angle : 0.749 5.498 5674 Z= 0.459 Chirality : 0.052 0.181 664 Planarity : 0.005 0.024 684 Dihedral : 11.166 75.301 1634 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.53 % Allowed : 1.05 % Favored : 98.42 % 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: -0.06 (0.34), residues: 518 helix: 0.30 (0.22), residues: 412 sheet: None (None), residues: 0 loop : -0.95 (0.70), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.021 0.004 TYR A 85 PHE 0.021 0.002 PHE A 202 TRP 0.009 0.002 TRP A 78 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.30 ( 4168) covalent geometry : angle 0.74907 / 0.46 ( 5674) hydrogen bonds : bond 0.10683 / 7.18 ( 336) hydrogen bonds : angle 5.55159 / 4.16 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8091 (tp30) cc_final: 0.7834 (tp30) REVERT: A 76 VAL cc_start: 0.8447 (m) cc_final: 0.8062 (p) REVERT: A 168 MET cc_start: 0.6991 (tpp) cc_final: 0.6595 (tpp) REVERT: A 255 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7871 (ttp80) REVERT: B 38 GLU cc_start: 0.8097 (tp30) cc_final: 0.7839 (tp30) REVERT: B 76 VAL cc_start: 0.8444 (m) cc_final: 0.8056 (p) REVERT: B 168 MET cc_start: 0.6996 (tpp) cc_final: 0.6594 (tpp) REVERT: B 255 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7876 (ttp80) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1108 time to fit residues: 11.1859 Evaluate side-chains 74 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.148728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.105492 restraints weight = 4831.648| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.58 r_work: 0.2867 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4168 Z= 0.154 Angle : 0.525 5.088 5674 Z= 0.297 Chirality : 0.039 0.166 664 Planarity : 0.003 0.023 684 Dihedral : 6.663 50.896 850 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.05 % Allowed : 7.89 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.37), residues: 518 helix: 2.64 (0.24), residues: 416 sheet: None (None), residues: 0 loop : 0.02 (0.75), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 36 TYR 0.014 0.002 TYR A 138 PHE 0.014 0.001 PHE B 109 TRP 0.012 0.002 TRP B 78 HIS 0.001 0.000 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4168) covalent geometry : angle 0.52471 / 0.30 ( 5674) hydrogen bonds : bond 0.04883 / 3.28 ( 336) hydrogen bonds : angle 3.46263 / 2.54 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8131 (tp30) cc_final: 0.7883 (tp30) REVERT: A 76 VAL cc_start: 0.8502 (m) cc_final: 0.8177 (p) REVERT: A 141 LYS cc_start: 0.7931 (tttt) cc_final: 0.7454 (tptt) REVERT: B 38 GLU cc_start: 0.8132 (tp30) cc_final: 0.7884 (tp30) REVERT: B 76 VAL cc_start: 0.8513 (m) cc_final: 0.8185 (p) REVERT: B 141 LYS cc_start: 0.7935 (tttt) cc_final: 0.7456 (tptt) outliers start: 4 outliers final: 2 residues processed: 82 average time/residue: 0.1015 time to fit residues: 9.6100 Evaluate side-chains 78 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain B residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.151128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.106974 restraints weight = 4743.679| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.57 r_work: 0.2895 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4168 Z= 0.124 Angle : 0.481 5.058 5674 Z= 0.267 Chirality : 0.037 0.143 664 Planarity : 0.003 0.019 684 Dihedral : 6.027 43.853 850 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.58 % Allowed : 7.89 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.91 (0.37), residues: 518 helix: 3.12 (0.24), residues: 418 sheet: None (None), residues: 0 loop : 0.11 (0.72), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 255 TYR 0.011 0.002 TYR A 138 PHE 0.013 0.001 PHE B 109 TRP 0.010 0.001 TRP B 78 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 4168) covalent geometry : angle 0.48127 / 0.27 ( 5674) hydrogen bonds : bond 0.04159 / 2.80 ( 336) hydrogen bonds : angle 3.19700 / 2.31 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7989 (tp30) cc_final: 0.7747 (tp30) REVERT: A 76 VAL cc_start: 0.8629 (m) cc_final: 0.8342 (p) REVERT: A 141 LYS cc_start: 0.7991 (tttt) cc_final: 0.7580 (tptt) REVERT: A 168 MET cc_start: 0.6916 (tpp) cc_final: 0.6710 (tpp) REVERT: B 38 GLU cc_start: 0.7996 (tp30) cc_final: 0.7754 (tp30) REVERT: B 76 VAL cc_start: 0.8631 (m) cc_final: 0.8348 (p) REVERT: B 141 LYS cc_start: 0.7998 (tttt) cc_final: 0.7585 (tptt) REVERT: B 168 MET cc_start: 0.6924 (tpp) cc_final: 0.6718 (tpp) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.1055 time to fit residues: 9.8727 Evaluate side-chains 78 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.146979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.102960 restraints weight = 4725.430| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.55 r_work: 0.2817 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4168 Z= 0.159 Angle : 0.519 5.195 5674 Z= 0.285 Chirality : 0.038 0.150 664 Planarity : 0.003 0.019 684 Dihedral : 5.888 48.385 850 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.84 % Allowed : 8.16 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.37), residues: 518 helix: 3.28 (0.24), residues: 416 sheet: None (None), residues: 0 loop : 0.16 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.018 0.002 TYR A 138 PHE 0.014 0.001 PHE B 109 TRP 0.007 0.001 TRP A 78 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 4168) covalent geometry : angle 0.51897 / 0.29 ( 5674) hydrogen bonds : bond 0.04275 / 2.88 ( 336) hydrogen bonds : angle 3.11532 / 2.26 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7956 (tp30) cc_final: 0.7721 (tp30) REVERT: A 76 VAL cc_start: 0.8593 (m) cc_final: 0.8317 (p) REVERT: A 168 MET cc_start: 0.6922 (tpp) cc_final: 0.6709 (tpp) REVERT: B 38 GLU cc_start: 0.7965 (tp30) cc_final: 0.7727 (tp30) REVERT: B 76 VAL cc_start: 0.8596 (m) cc_final: 0.8321 (p) REVERT: B 168 MET cc_start: 0.6925 (tpp) cc_final: 0.6714 (tpp) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.0850 time to fit residues: 7.6376 Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 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 = 0.3652 r_free = 0.3652 target = 0.147523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103126 restraints weight = 4744.314| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.56 r_work: 0.2846 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4168 Z= 0.153 Angle : 0.526 7.300 5674 Z= 0.281 Chirality : 0.038 0.150 664 Planarity : 0.003 0.019 684 Dihedral : 5.807 53.339 850 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.11 % Allowed : 10.00 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.17 (0.37), residues: 518 helix: 3.32 (0.24), residues: 416 sheet: None (None), residues: 0 loop : 0.18 (0.71), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 255 TYR 0.021 0.002 TYR A 138 PHE 0.014 0.001 PHE A 109 TRP 0.007 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 4168) covalent geometry : angle 0.52603 / 0.28 ( 5674) hydrogen bonds : bond 0.04181 / 2.82 ( 336) hydrogen bonds : angle 3.07786 / 2.24 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.8633 (m) cc_final: 0.8427 (p) REVERT: A 138 TYR cc_start: 0.7751 (t80) cc_final: 0.7225 (t80) REVERT: A 142 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.6604 (ttm-80) REVERT: A 168 MET cc_start: 0.6911 (tpp) cc_final: 0.6699 (tpp) REVERT: B 76 VAL cc_start: 0.8633 (m) cc_final: 0.8426 (p) REVERT: B 138 TYR cc_start: 0.7759 (t80) cc_final: 0.7229 (t80) REVERT: B 142 ARG cc_start: 0.7305 (ttt-90) cc_final: 0.6611 (ttm-80) REVERT: B 168 MET cc_start: 0.6918 (tpp) cc_final: 0.6706 (tpp) outliers start: 8 outliers final: 8 residues processed: 78 average time/residue: 0.0776 time to fit residues: 7.0832 Evaluate side-chains 80 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.145406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.100255 restraints weight = 4904.628| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.57 r_work: 0.2911 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4168 Z= 0.127 Angle : 0.500 5.730 5674 Z= 0.268 Chirality : 0.036 0.141 664 Planarity : 0.003 0.019 684 Dihedral : 5.740 58.929 850 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.32 % Allowed : 9.74 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.37), residues: 518 helix: 3.43 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.06 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 255 TYR 0.016 0.001 TYR A 138 PHE 0.018 0.001 PHE B 109 TRP 0.008 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 4168) covalent geometry : angle 0.50003 / 0.27 ( 5674) hydrogen bonds : bond 0.03911 / 2.64 ( 336) hydrogen bonds : angle 2.97402 / 2.15 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.115 Fit side-chains REVERT: A 76 VAL cc_start: 0.8779 (m) cc_final: 0.8553 (p) REVERT: A 138 TYR cc_start: 0.7793 (t80) cc_final: 0.7235 (t80) REVERT: A 141 LYS cc_start: 0.8073 (tttt) cc_final: 0.7870 (tppt) REVERT: A 142 ARG cc_start: 0.7342 (ttt-90) cc_final: 0.6631 (ttm-80) REVERT: A 168 MET cc_start: 0.7036 (tpp) cc_final: 0.6819 (tpp) REVERT: B 76 VAL cc_start: 0.8782 (m) cc_final: 0.8554 (p) REVERT: B 138 TYR cc_start: 0.7791 (t80) cc_final: 0.7226 (t80) REVERT: B 141 LYS cc_start: 0.8073 (tttt) cc_final: 0.7868 (tppt) REVERT: B 142 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.6631 (ttm-80) REVERT: B 168 MET cc_start: 0.7032 (tpp) cc_final: 0.6817 (tpp) outliers start: 5 outliers final: 5 residues processed: 73 average time/residue: 0.0810 time to fit residues: 6.9006 Evaluate side-chains 75 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.145967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100700 restraints weight = 4838.805| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.56 r_work: 0.2916 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4168 Z= 0.131 Angle : 0.510 5.498 5674 Z= 0.274 Chirality : 0.036 0.151 664 Planarity : 0.003 0.021 684 Dihedral : 5.631 56.259 850 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.32 % Allowed : 9.74 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.37), residues: 518 helix: 3.47 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.22 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 255 TYR 0.013 0.002 TYR B 138 PHE 0.020 0.001 PHE A 109 TRP 0.006 0.001 TRP A 78 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4168) covalent geometry : angle 0.50987 / 0.27 ( 5674) hydrogen bonds : bond 0.03935 / 2.66 ( 336) hydrogen bonds : angle 2.96694 / 2.16 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.085 Fit side-chains REVERT: A 76 VAL cc_start: 0.8764 (m) cc_final: 0.8542 (p) REVERT: A 138 TYR cc_start: 0.7763 (t80) cc_final: 0.7208 (t80) REVERT: A 141 LYS cc_start: 0.8067 (tttt) cc_final: 0.7852 (tppt) REVERT: A 142 ARG cc_start: 0.7341 (ttt-90) cc_final: 0.6619 (ttm-80) REVERT: A 168 MET cc_start: 0.7003 (tpp) cc_final: 0.6798 (tpp) REVERT: B 76 VAL cc_start: 0.8767 (m) cc_final: 0.8541 (p) REVERT: B 138 TYR cc_start: 0.7762 (t80) cc_final: 0.7201 (t80) REVERT: B 141 LYS cc_start: 0.8063 (tttt) cc_final: 0.7848 (tppt) REVERT: B 142 ARG cc_start: 0.7339 (ttt-90) cc_final: 0.6616 (ttm-80) REVERT: B 168 MET cc_start: 0.6997 (tpp) cc_final: 0.6794 (tpp) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.0716 time to fit residues: 6.2570 Evaluate side-chains 77 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.0050 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.148345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103622 restraints weight = 4763.240| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.54 r_work: 0.2971 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4168 Z= 0.111 Angle : 0.491 5.300 5674 Z= 0.264 Chirality : 0.035 0.153 664 Planarity : 0.003 0.024 684 Dihedral : 5.412 51.995 850 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.05 % Allowed : 9.47 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.38), residues: 518 helix: 3.55 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.28 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 255 TYR 0.012 0.001 TYR B 138 PHE 0.018 0.001 PHE B 109 TRP 0.008 0.002 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 4168) covalent geometry : angle 0.49120 / 0.26 ( 5674) hydrogen bonds : bond 0.03639 / 2.46 ( 336) hydrogen bonds : angle 2.88488 / 2.09 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.145 Fit side-chains REVERT: A 38 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 138 TYR cc_start: 0.7760 (t80) cc_final: 0.7210 (t80) REVERT: A 142 ARG cc_start: 0.7347 (ttt-90) cc_final: 0.6636 (ttm-80) REVERT: B 38 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 138 TYR cc_start: 0.7754 (t80) cc_final: 0.7204 (t80) REVERT: B 142 ARG cc_start: 0.7344 (ttt-90) cc_final: 0.6630 (ttm-80) outliers start: 4 outliers final: 4 residues processed: 76 average time/residue: 0.1017 time to fit residues: 9.0561 Evaluate side-chains 74 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.147256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.101202 restraints weight = 4901.409| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.60 r_work: 0.2906 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4168 Z= 0.144 Angle : 0.522 5.450 5674 Z= 0.282 Chirality : 0.038 0.163 664 Planarity : 0.003 0.024 684 Dihedral : 5.432 48.855 850 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.05 % Allowed : 11.58 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.37), residues: 518 helix: 3.44 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.21 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 255 TYR 0.012 0.001 TYR A 113 PHE 0.020 0.001 PHE B 109 TRP 0.006 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4168) covalent geometry : angle 0.52220 / 0.28 ( 5674) hydrogen bonds : bond 0.03923 / 2.65 ( 336) hydrogen bonds : angle 2.98415 / 2.16 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.122 Fit side-chains REVERT: A 38 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 138 TYR cc_start: 0.7712 (t80) cc_final: 0.7237 (t80) REVERT: A 142 ARG cc_start: 0.7240 (ttt-90) cc_final: 0.6546 (ttm-80) REVERT: B 38 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 138 TYR cc_start: 0.7706 (t80) cc_final: 0.7224 (t80) REVERT: B 142 ARG cc_start: 0.7234 (ttt-90) cc_final: 0.6538 (ttm-80) outliers start: 4 outliers final: 4 residues processed: 72 average time/residue: 0.0943 time to fit residues: 7.8841 Evaluate side-chains 74 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.146766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101557 restraints weight = 4821.462| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.54 r_work: 0.2906 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4168 Z= 0.144 Angle : 0.536 5.995 5674 Z= 0.288 Chirality : 0.038 0.162 664 Planarity : 0.003 0.023 684 Dihedral : 5.387 45.715 850 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.58 % Allowed : 11.05 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.37), residues: 518 helix: 3.32 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.26 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.013 0.001 TYR A 138 PHE 0.020 0.002 PHE B 109 TRP 0.006 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4168) covalent geometry : angle 0.53550 / 0.29 ( 5674) hydrogen bonds : bond 0.03995 / 2.70 ( 336) hydrogen bonds : angle 3.04159 / 2.21 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1036 Ramachandran restraints generated. 518 Oldfield, 0 Emsley, 518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.108 Fit side-chains REVERT: A 38 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 138 TYR cc_start: 0.7760 (t80) cc_final: 0.7316 (t80) REVERT: A 141 LYS cc_start: 0.7736 (tppt) cc_final: 0.7395 (tptt) REVERT: A 142 ARG cc_start: 0.7170 (ttt-90) cc_final: 0.6576 (ttm-80) REVERT: B 38 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 138 TYR cc_start: 0.7760 (t80) cc_final: 0.7315 (t80) REVERT: B 141 LYS cc_start: 0.7727 (tppt) cc_final: 0.7391 (tptt) REVERT: B 142 ARG cc_start: 0.7162 (ttt-90) cc_final: 0.6567 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 0.0983 time to fit residues: 8.6765 Evaluate side-chains 82 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 249 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.145798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101022 restraints weight = 4835.704| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.52 r_work: 0.2923 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4168 Z= 0.134 Angle : 0.528 6.000 5674 Z= 0.283 Chirality : 0.037 0.158 664 Planarity : 0.003 0.024 684 Dihedral : 5.363 43.155 850 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.05 % Allowed : 12.11 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.37), residues: 518 helix: 3.37 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.38 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 255 TYR 0.011 0.001 TYR B 138 PHE 0.020 0.001 PHE B 164 TRP 0.006 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 4168) covalent geometry : angle 0.52772 / 0.28 ( 5674) hydrogen bonds : bond 0.03862 / 2.61 ( 336) hydrogen bonds : angle 3.00810 / 2.18 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 948.04 seconds wall clock time: 16 minutes 56.43 seconds (1016.43 seconds total)