Starting phenix.real_space_refine on Wed Aug 5 03:14:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31cj_58290/08_2026/31cj_58290_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/31cj_58290/08_2026/31cj_58290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31cj_58290/08_2026/31cj_58290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31cj_58290/08_2026/31cj_58290.map" model { file = "/net/cci-nas-00/data/ceres_data/31cj_58290/08_2026/31cj_58290_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31cj_58290/08_2026/31cj_58290_trim.cif" } resolution = 3.3 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 26 5.16 5 C 2550 2.51 5 N 722 2.21 5 O 716 1.98 5 H 3988 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8006 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3950 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 3.24, per 1000 atoms: 0.40 Number of scatterers: 8006 At special positions: 0 Unit cell: (91.52, 63.36, 93.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 4 15.00 O 716 8.00 N 722 7.00 C 2550 6.00 H 3988 1.00 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: 0.67 Conformation dependent library (CDL) restraints added in 282.1 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 55.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.589A pdb=" N GLY A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.752A pdb=" N PHE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 136 Proline residue: A 128 - end of helix removed outlier: 3.778A pdb=" N ALA A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 160 through 183 removed outlier: 3.684A pdb=" N ARG A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 208 removed outlier: 4.138A pdb=" N TYR A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.589A pdb=" N GLY B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 62 through 76 removed outlier: 3.752A pdb=" N PHE B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 136 Proline residue: B 128 - end of helix removed outlier: 3.778A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 160 through 183 removed outlier: 3.684A pdb=" N ARG B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 208 removed outlier: 4.138A pdb=" N TYR B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 237 through 251 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.299A pdb=" N THR A 23 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 33 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET A 102 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR A 111 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 100 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 113 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN A 98 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG A 115 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG A 96 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 143 Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.299A pdb=" N THR B 23 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA B 33 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET B 102 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR B 111 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 100 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER B 113 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN B 98 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG B 115 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ARG B 96 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 143 224 hydrogen bonds defined for protein. 624 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: 1.68 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3984 1.03 - 1.23: 6 1.23 - 1.42: 1696 1.42 - 1.61: 2372 1.61 - 1.81: 46 Bond restraints: 8104 Sorted by residual: bond pdb=" C4 FAD B 601 " pdb=" C4X FAD B 601 " ideal model delta sigma weight residual 1.481 1.408 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C4 FAD A 601 " pdb=" C4X FAD A 601 " ideal model delta sigma weight residual 1.481 1.408 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.660 1.596 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.660 1.596 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O5' FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.637 1.587 0.050 2.00e-02 2.50e+03 6.16e+00 ... (remaining 8099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 14144 1.25 - 2.49: 426 2.49 - 3.74: 46 3.74 - 4.98: 10 4.98 - 6.23: 10 Bond angle restraints: 14636 Sorted by residual: angle pdb=" N VAL A 183 " pdb=" CA VAL A 183 " pdb=" C VAL A 183 " ideal model delta sigma weight residual 112.80 110.22 2.58 1.15e+00 7.56e-01 5.03e+00 angle pdb=" N VAL B 183 " pdb=" CA VAL B 183 " pdb=" C VAL B 183 " ideal model delta sigma weight residual 112.80 110.22 2.58 1.15e+00 7.56e-01 5.03e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O5B FAD B 601 " ideal model delta sigma weight residual 104.10 110.33 -6.23 3.00e+00 1.11e-01 4.31e+00 angle pdb=" O1A FAD A 601 " pdb=" PA FAD A 601 " pdb=" O5B FAD A 601 " ideal model delta sigma weight residual 104.10 110.33 -6.23 3.00e+00 1.11e-01 4.31e+00 angle pdb=" C3' FAD B 601 " pdb=" C4' FAD B 601 " pdb=" O4' FAD B 601 " ideal model delta sigma weight residual 107.24 113.43 -6.19 3.00e+00 1.11e-01 4.26e+00 ... (remaining 14631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 3450 21.02 - 42.03: 258 42.03 - 63.05: 94 63.05 - 84.06: 14 84.06 - 105.08: 2 Dihedral angle restraints: 3818 sinusoidal: 2140 harmonic: 1678 Sorted by residual: dihedral pdb=" O5' FAD B 601 " pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sinusoidal sigma weight residual -61.77 43.31 -105.08 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" O5' FAD A 601 " pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sinusoidal sigma weight residual -61.77 43.31 -105.08 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" N ARG B 164 " pdb=" CA ARG B 164 " pdb=" CB ARG B 164 " pdb=" CG ARG B 164 " ideal model delta sinusoidal sigma weight residual -180.00 -120.89 -59.11 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 388 0.028 - 0.055: 148 0.055 - 0.083: 58 0.083 - 0.111: 24 0.111 - 0.138: 14 Chirality restraints: 632 Sorted by residual: chirality pdb=" CA ILE B 114 " pdb=" N ILE B 114 " pdb=" C ILE B 114 " pdb=" CB ILE B 114 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A 114 " pdb=" N ILE A 114 " pdb=" C ILE A 114 " pdb=" CB ILE A 114 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL A 100 " pdb=" N VAL A 100 " pdb=" C VAL A 100 " pdb=" CB VAL A 100 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 629 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 210 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 211 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 210 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 211 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1B FAD A 601 " -0.019 2.00e-02 2.50e+03 8.09e-03 1.80e+00 pdb=" C2A FAD A 601 " 0.001 2.00e-02 2.50e+03 pdb=" C4A FAD A 601 " 0.009 2.00e-02 2.50e+03 pdb=" C5A FAD A 601 " 0.005 2.00e-02 2.50e+03 pdb=" C6A FAD A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C8A FAD A 601 " 0.000 2.00e-02 2.50e+03 pdb=" N1A FAD A 601 " -0.006 2.00e-02 2.50e+03 pdb=" N3A FAD A 601 " 0.007 2.00e-02 2.50e+03 pdb=" N6A FAD A 601 " -0.011 2.00e-02 2.50e+03 pdb=" N7A FAD A 601 " 0.004 2.00e-02 2.50e+03 pdb=" N9A FAD A 601 " 0.008 2.00e-02 2.50e+03 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.00: 37 2.00 - 2.65: 11029 2.65 - 3.30: 24043 3.30 - 3.95: 30020 3.95 - 4.60: 47015 Nonbonded interactions: 112144 Sorted by model distance: nonbonded pdb="HD13 ILE A 212 " pdb="HD11 ILE B 212 " model vdw 1.355 2.440 nonbonded pdb="HD11 ILE A 212 " pdb="HD13 ILE B 212 " model vdw 1.355 2.440 nonbonded pdb=" HE1 MET A 172 " pdb=" HE1 MET B 172 " model vdw 1.411 2.440 nonbonded pdb="HG13 VAL A 168 " pdb=" HE2 PHE B 204 " model vdw 1.624 2.270 nonbonded pdb=" HE2 PHE A 204 " pdb="HG13 VAL B 168 " model vdw 1.624 2.270 ... (remaining 112139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.090 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: 0.050 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 0.073 4116 Z= 0.204 Angle : 0.571 6.226 5610 Z= 0.266 Chirality : 0.040 0.138 632 Planarity : 0.004 0.037 688 Dihedral : 17.133 105.077 1562 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.48 % Allowed : 9.62 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.41), residues: 492 helix: 1.92 (0.37), residues: 234 sheet: -2.56 (0.53), residues: 70 loop : 1.70 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 164 TYR 0.005 0.001 TYR B 93 PHE 0.005 0.001 PHE A 173 TRP 0.006 0.001 TRP A 70 HIS 0.002 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 ( 4116) covalent geometry : angle 0.57105 / 0.27 ( 5610) hydrogen bonds : bond 0.15835 / 10.00 ( 224) hydrogen bonds : angle 6.16536 / 4.43 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 160 average time/residue: 0.1532 time to fit residues: 30.9671 Evaluate side-chains 113 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 251 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.067004 restraints weight = 30269.760| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.67 r_work: 0.2830 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4116 Z= 0.149 Angle : 0.530 4.103 5610 Z= 0.276 Chirality : 0.039 0.137 632 Planarity : 0.004 0.038 688 Dihedral : 9.598 91.954 640 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.68 % Allowed : 19.47 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.40), residues: 492 helix: 1.87 (0.36), residues: 250 sheet: -2.28 (0.54), residues: 70 loop : 1.68 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.016 0.002 TYR A 29 PHE 0.006 0.001 PHE A 71 TRP 0.008 0.001 TRP A 94 HIS 0.006 0.002 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 4116) covalent geometry : angle 0.53042 / 0.28 ( 5610) hydrogen bonds : bond 0.03248 / 2.17 ( 224) hydrogen bonds : angle 4.37368 / 3.19 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6861 (ttt) cc_final: 0.6276 (tmm) REVERT: A 51 GLN cc_start: 0.8527 (mm110) cc_final: 0.8188 (mm110) REVERT: A 112 MET cc_start: 0.8777 (ttm) cc_final: 0.8504 (ttp) REVERT: B 21 MET cc_start: 0.6868 (ttt) cc_final: 0.6280 (tmm) REVERT: B 51 GLN cc_start: 0.8524 (mm110) cc_final: 0.8186 (mm110) REVERT: B 112 MET cc_start: 0.8784 (ttm) cc_final: 0.8513 (ttp) outliers start: 7 outliers final: 2 residues processed: 119 average time/residue: 0.0991 time to fit residues: 16.2535 Evaluate side-chains 112 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.077426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.065449 restraints weight = 29866.339| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.76 r_work: 0.2798 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4116 Z= 0.118 Angle : 0.492 3.894 5610 Z= 0.258 Chirality : 0.038 0.139 632 Planarity : 0.004 0.036 688 Dihedral : 8.739 90.014 640 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.40 % Allowed : 21.15 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.40), residues: 492 helix: 1.96 (0.35), residues: 250 sheet: -2.26 (0.53), residues: 70 loop : 1.55 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 137 TYR 0.013 0.001 TYR A 29 PHE 0.004 0.001 PHE B 37 TRP 0.006 0.001 TRP A 94 HIS 0.005 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4116) covalent geometry : angle 0.49208 / 0.26 ( 5610) hydrogen bonds : bond 0.02875 / 1.93 ( 224) hydrogen bonds : angle 3.98987 / 2.92 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7031 (ttt) cc_final: 0.6366 (tmm) REVERT: A 112 MET cc_start: 0.8752 (ttm) cc_final: 0.8474 (ttp) REVERT: B 21 MET cc_start: 0.7053 (ttt) cc_final: 0.6383 (tmm) REVERT: B 112 MET cc_start: 0.8748 (ttm) cc_final: 0.8470 (ttp) outliers start: 10 outliers final: 9 residues processed: 122 average time/residue: 0.1019 time to fit residues: 17.1851 Evaluate side-chains 120 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065094 restraints weight = 30760.946| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.76 r_work: 0.2790 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4116 Z= 0.128 Angle : 0.491 3.914 5610 Z= 0.253 Chirality : 0.038 0.136 632 Planarity : 0.004 0.037 688 Dihedral : 8.363 81.766 640 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 21.88 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.40), residues: 492 helix: 2.09 (0.35), residues: 250 sheet: -2.25 (0.55), residues: 70 loop : 1.62 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.010 0.001 TYR A 29 PHE 0.004 0.001 PHE B 173 TRP 0.006 0.001 TRP A 163 HIS 0.005 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4116) covalent geometry : angle 0.49088 / 0.25 ( 5610) hydrogen bonds : bond 0.02746 / 1.84 ( 224) hydrogen bonds : angle 3.83615 / 2.80 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7093 (ttt) cc_final: 0.6391 (tmm) REVERT: A 46 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8505 (tm-30) REVERT: B 21 MET cc_start: 0.7111 (ttt) cc_final: 0.6406 (tmm) REVERT: B 46 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8501 (tm-30) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 0.1064 time to fit residues: 17.3191 Evaluate side-chains 115 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.063700 restraints weight = 30568.120| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.57 r_work: 0.2762 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4116 Z= 0.230 Angle : 0.553 4.033 5610 Z= 0.291 Chirality : 0.039 0.136 632 Planarity : 0.005 0.038 688 Dihedral : 8.617 87.214 636 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 21.15 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.40), residues: 492 helix: 2.06 (0.35), residues: 250 sheet: -2.19 (0.56), residues: 70 loop : 1.28 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 137 TYR 0.008 0.001 TYR B 29 PHE 0.006 0.002 PHE A 173 TRP 0.006 0.001 TRP B 163 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 ( 4116) covalent geometry : angle 0.55290 / 0.29 ( 5610) hydrogen bonds : bond 0.02979 / 1.99 ( 224) hydrogen bonds : angle 4.01039 / 2.91 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7119 (ttt) cc_final: 0.6405 (tmm) REVERT: A 46 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8514 (tm-30) REVERT: B 21 MET cc_start: 0.7145 (ttt) cc_final: 0.6425 (tmm) REVERT: B 46 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8509 (tm-30) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 0.1083 time to fit residues: 17.4899 Evaluate side-chains 111 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN B 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065389 restraints weight = 29937.784| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.56 r_work: 0.2803 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4116 Z= 0.116 Angle : 0.498 3.893 5610 Z= 0.258 Chirality : 0.038 0.135 632 Planarity : 0.005 0.051 688 Dihedral : 8.164 82.766 636 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.64 % Allowed : 21.39 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.40), residues: 492 helix: 2.14 (0.35), residues: 250 sheet: -2.17 (0.55), residues: 70 loop : 1.45 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 137 TYR 0.007 0.001 TYR B 29 PHE 0.006 0.001 PHE A 37 TRP 0.005 0.001 TRP A 163 HIS 0.005 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 4116) covalent geometry : angle 0.49752 / 0.26 ( 5610) hydrogen bonds : bond 0.02688 / 1.79 ( 224) hydrogen bonds : angle 3.75747 / 2.74 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7199 (ttt) cc_final: 0.6468 (tmm) REVERT: A 51 GLN cc_start: 0.8671 (mm110) cc_final: 0.8381 (mm110) REVERT: B 21 MET cc_start: 0.7222 (ttt) cc_final: 0.6490 (tmm) REVERT: B 51 GLN cc_start: 0.8666 (mm110) cc_final: 0.8375 (mm110) outliers start: 11 outliers final: 8 residues processed: 122 average time/residue: 0.1123 time to fit residues: 18.0638 Evaluate side-chains 116 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN B 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.077824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066714 restraints weight = 30158.704| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.56 r_work: 0.2815 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4116 Z= 0.125 Angle : 0.501 3.885 5610 Z= 0.260 Chirality : 0.038 0.135 632 Planarity : 0.005 0.054 688 Dihedral : 7.890 78.026 636 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.16 % Allowed : 22.84 % Favored : 75.00 % 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: 1.79 (0.40), residues: 492 helix: 2.18 (0.35), residues: 250 sheet: -2.14 (0.54), residues: 70 loop : 1.43 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 137 TYR 0.008 0.001 TYR A 29 PHE 0.004 0.001 PHE A 37 TRP 0.005 0.001 TRP B 163 HIS 0.005 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 4116) covalent geometry : angle 0.50053 / 0.26 ( 5610) hydrogen bonds : bond 0.02661 / 1.78 ( 224) hydrogen bonds : angle 3.70894 / 2.71 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6966 (ttt) cc_final: 0.6253 (tmm) REVERT: A 51 GLN cc_start: 0.8595 (mm110) cc_final: 0.8282 (mm110) REVERT: B 21 MET cc_start: 0.6969 (ttt) cc_final: 0.6273 (tmm) REVERT: B 51 GLN cc_start: 0.8583 (mm110) cc_final: 0.8269 (mm110) outliers start: 9 outliers final: 9 residues processed: 116 average time/residue: 0.1101 time to fit residues: 17.4292 Evaluate side-chains 105 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.067044 restraints weight = 29871.253| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.52 r_work: 0.2822 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4116 Z= 0.129 Angle : 0.505 3.849 5610 Z= 0.261 Chirality : 0.038 0.132 632 Planarity : 0.005 0.060 688 Dihedral : 7.826 76.213 636 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.92 % Allowed : 22.60 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.40), residues: 492 helix: 2.19 (0.35), residues: 250 sheet: -2.19 (0.52), residues: 74 loop : 1.49 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 137 TYR 0.007 0.001 TYR A 29 PHE 0.004 0.001 PHE A 173 TRP 0.005 0.001 TRP B 163 HIS 0.004 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 4116) covalent geometry : angle 0.50470 / 0.26 ( 5610) hydrogen bonds : bond 0.02629 / 1.76 ( 224) hydrogen bonds : angle 3.68336 / 2.68 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6938 (ttt) cc_final: 0.6215 (tmm) REVERT: A 51 GLN cc_start: 0.8600 (mm110) cc_final: 0.8277 (mm110) REVERT: B 21 MET cc_start: 0.6944 (ttt) cc_final: 0.6265 (tmm) REVERT: B 51 GLN cc_start: 0.8593 (mm110) cc_final: 0.8276 (mm110) outliers start: 8 outliers final: 8 residues processed: 116 average time/residue: 0.1087 time to fit residues: 17.2281 Evaluate side-chains 114 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN B 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.076902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.065771 restraints weight = 30223.370| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.53 r_work: 0.2795 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4116 Z= 0.209 Angle : 0.551 3.883 5610 Z= 0.287 Chirality : 0.039 0.135 632 Planarity : 0.006 0.075 688 Dihedral : 8.257 80.748 636 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.92 % Allowed : 24.28 % Favored : 73.80 % 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: 1.62 (0.39), residues: 492 helix: 2.11 (0.35), residues: 250 sheet: -2.15 (0.53), residues: 74 loop : 1.29 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 137 TYR 0.007 0.001 TYR B 29 PHE 0.015 0.002 PHE B 37 TRP 0.006 0.001 TRP B 163 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 ( 4116) covalent geometry : angle 0.55063 / 0.29 ( 5610) hydrogen bonds : bond 0.02830 / 1.89 ( 224) hydrogen bonds : angle 3.84713 / 2.80 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6911 (ttt) cc_final: 0.6188 (tmm) REVERT: A 51 GLN cc_start: 0.8647 (mm110) cc_final: 0.8373 (mm110) REVERT: A 112 MET cc_start: 0.8626 (ttm) cc_final: 0.8383 (ttp) REVERT: A 234 ASN cc_start: 0.9238 (m-40) cc_final: 0.8532 (p0) REVERT: B 21 MET cc_start: 0.6975 (ttt) cc_final: 0.6253 (tmm) REVERT: B 51 GLN cc_start: 0.8647 (mm110) cc_final: 0.8366 (mm110) outliers start: 8 outliers final: 8 residues processed: 113 average time/residue: 0.1104 time to fit residues: 17.1016 Evaluate side-chains 102 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.078756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067894 restraints weight = 29668.237| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.45 r_work: 0.2823 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4116 Z= 0.130 Angle : 0.516 3.915 5610 Z= 0.267 Chirality : 0.038 0.134 632 Planarity : 0.006 0.069 688 Dihedral : 8.014 78.733 636 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.92 % Allowed : 24.28 % Favored : 73.80 % 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: 1.77 (0.40), residues: 492 helix: 2.22 (0.35), residues: 250 sheet: -2.13 (0.53), residues: 74 loop : 1.41 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 137 TYR 0.006 0.001 TYR A 43 PHE 0.009 0.001 PHE B 37 TRP 0.005 0.001 TRP B 163 HIS 0.004 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 4116) covalent geometry : angle 0.51615 / 0.27 ( 5610) hydrogen bonds : bond 0.02649 / 1.77 ( 224) hydrogen bonds : angle 3.69984 / 2.70 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6913 (ttt) cc_final: 0.6223 (tmm) REVERT: A 51 GLN cc_start: 0.8630 (mm110) cc_final: 0.8357 (mm110) REVERT: A 112 MET cc_start: 0.8600 (ttm) cc_final: 0.8368 (ttp) REVERT: A 205 GLU cc_start: 0.9086 (tt0) cc_final: 0.8880 (mt-10) REVERT: A 234 ASN cc_start: 0.9189 (m-40) cc_final: 0.8460 (p0) REVERT: B 21 MET cc_start: 0.6960 (ttt) cc_final: 0.6244 (tmm) REVERT: B 51 GLN cc_start: 0.8630 (mm110) cc_final: 0.8330 (mm110) REVERT: B 205 GLU cc_start: 0.9091 (tt0) cc_final: 0.8885 (mt-10) REVERT: B 234 ASN cc_start: 0.9190 (m-40) cc_final: 0.8473 (p0) outliers start: 8 outliers final: 8 residues processed: 116 average time/residue: 0.1056 time to fit residues: 16.9694 Evaluate side-chains 115 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.079360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.068502 restraints weight = 29678.812| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.48 r_work: 0.2838 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4116 Z= 0.114 Angle : 0.512 4.090 5610 Z= 0.264 Chirality : 0.038 0.135 632 Planarity : 0.006 0.073 688 Dihedral : 7.785 74.192 636 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.68 % Allowed : 24.76 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.40), residues: 492 helix: 2.30 (0.35), residues: 250 sheet: -2.06 (0.53), residues: 74 loop : 1.44 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 137 TYR 0.006 0.001 TYR B 43 PHE 0.009 0.001 PHE A 37 TRP 0.005 0.001 TRP B 163 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 4116) covalent geometry : angle 0.51223 / 0.26 ( 5610) hydrogen bonds : bond 0.02587 / 1.73 ( 224) hydrogen bonds : angle 3.60859 / 2.63 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.94 seconds wall clock time: 38 minutes 45.00 seconds (2325.00 seconds total)