Starting phenix.real_space_refine on Thu Jul 2 07:17:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzp_49955/07_2026/9nzp_49955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzp_49955/07_2026/9nzp_49955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nzp_49955/07_2026/9nzp_49955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzp_49955/07_2026/9nzp_49955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nzp_49955/07_2026/9nzp_49955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzp_49955/07_2026/9nzp_49955.map" } resolution = 3.07 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 199 5.49 5 S 14 5.16 5 C 3929 2.51 5 N 1327 2.21 5 O 1928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7397 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1596 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 2, 'TRANS': 192} Chain: "B" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1588 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 2, 'TRANS': 191} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3399 Classifications: {'RNA': 159} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 77, 'rna3p_pyr': 58} Link IDs: {'rna2p': 24, 'rna3p': 134} Time building chain proxies: 1.75, per 1000 atoms: 0.24 Number of scatterers: 7397 At special positions: 0 Unit cell: (101.26, 87.98, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 199 15.00 O 1928 8.00 N 1327 7.00 C 3929 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: 0.68 Conformation dependent library (CDL) restraints added in 322.4 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 742 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 4 sheets defined 44.2% alpha, 19.8% beta 56 base pairs and 110 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 15 through 47 removed outlier: 4.005A pdb=" N SER A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.500A pdb=" N PHE A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.824A pdb=" N SER A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'B' and resid 15 through 46 removed outlier: 3.655A pdb=" N ALA B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.710A pdb=" N LYS B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 147 through 152 removed outlier: 4.605A pdb=" N TYR B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 3.559A pdb=" N ARG B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.620A pdb=" N LEU A 114 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 176 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 185 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.620A pdb=" N LEU A 114 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 176 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 171 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.552A pdb=" N SER B 176 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.552A pdb=" N SER B 176 " --> pdb=" O ASN B 188 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 143 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 110 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1478 1.34 - 1.46: 2885 1.46 - 1.58: 3166 1.58 - 1.70: 395 1.70 - 1.82: 24 Bond restraints: 7948 Sorted by residual: bond pdb=" N9 A E 90 " pdb=" C4 A E 90 " ideal model delta sigma weight residual 1.374 1.403 -0.029 6.00e-03 2.78e+04 2.38e+01 bond pdb=" C1' DC C 18 " pdb=" N1 DC C 18 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" N9 G E 16 " pdb=" C4 G E 16 " ideal model delta sigma weight residual 1.375 1.349 0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C1' DC C 11 " pdb=" N1 DC C 11 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C5' DT C 17 " pdb=" C4' DT C 17 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 1.02e+01 ... (remaining 7943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 10922 2.12 - 4.24: 613 4.24 - 6.36: 81 6.36 - 8.48: 30 8.48 - 10.60: 9 Bond angle restraints: 11655 Sorted by residual: angle pdb=" C2 C E 17 " pdb=" N1 C E 17 " pdb=" C6 C E 17 " ideal model delta sigma weight residual 120.30 117.01 3.29 4.00e-01 6.25e+00 6.77e+01 angle pdb=" C1' C E 93 " pdb=" N1 C E 93 " pdb=" C2 C E 93 " ideal model delta sigma weight residual 118.80 126.68 -7.88 1.10e+00 8.26e-01 5.13e+01 angle pdb=" C2 A E 137 " pdb=" N3 A E 137 " pdb=" C4 A E 137 " ideal model delta sigma weight residual 110.60 114.05 -3.45 5.00e-01 4.00e+00 4.75e+01 angle pdb=" N9 G E 29 " pdb=" C8 G E 29 " pdb=" N7 G E 29 " ideal model delta sigma weight residual 113.10 116.30 -3.20 5.00e-01 4.00e+00 4.09e+01 angle pdb=" N1 U E 10 " pdb=" C6 U E 10 " pdb=" C5 U E 10 " ideal model delta sigma weight residual 122.70 125.86 -3.16 5.00e-01 4.00e+00 4.00e+01 ... (remaining 11650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 4148 34.74 - 69.47: 637 69.47 - 104.21: 65 104.21 - 138.95: 5 138.95 - 173.68: 9 Dihedral angle restraints: 4864 sinusoidal: 3715 harmonic: 1149 Sorted by residual: dihedral pdb=" O4' U E 53 " pdb=" C1' U E 53 " pdb=" N1 U E 53 " pdb=" C2 U E 53 " ideal model delta sinusoidal sigma weight residual 200.00 50.66 149.34 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' C E 110 " pdb=" C1' C E 110 " pdb=" N1 C E 110 " pdb=" C2 C E 110 " ideal model delta sinusoidal sigma weight residual 232.00 58.32 173.68 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U E 106 " pdb=" C1' U E 106 " pdb=" N1 U E 106 " pdb=" C2 U E 106 " ideal model delta sinusoidal sigma weight residual 232.00 61.16 170.84 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 4861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1100 0.060 - 0.121: 267 0.121 - 0.181: 45 0.181 - 0.242: 14 0.242 - 0.302: 6 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' U E 9 " pdb=" C4' U E 9 " pdb=" O3' U E 9 " pdb=" C2' U E 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C4' U E 136 " pdb=" C5' U E 136 " pdb=" O4' U E 136 " pdb=" C3' U E 136 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" P G E 49 " pdb=" OP1 G E 49 " pdb=" OP2 G E 49 " pdb=" O5' G E 49 " both_signs ideal model delta sigma weight residual True 2.41 -2.66 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1429 not shown) Planarity restraints: 745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C E 2 " 0.030 2.00e-02 2.50e+03 3.05e-02 2.09e+01 pdb=" N1 C E 2 " -0.074 2.00e-02 2.50e+03 pdb=" C2 C E 2 " 0.041 2.00e-02 2.50e+03 pdb=" O2 C E 2 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C E 2 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C E 2 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C E 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C E 2 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C E 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 38 " 0.043 2.00e-02 2.50e+03 2.20e-02 1.33e+01 pdb=" N9 A E 38 " -0.057 2.00e-02 2.50e+03 pdb=" C8 A E 38 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A E 38 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A E 38 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A E 38 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A E 38 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A E 38 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A E 38 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A E 38 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A E 38 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 53 " 0.046 2.00e-02 2.50e+03 2.40e-02 1.29e+01 pdb=" N1 U E 53 " -0.051 2.00e-02 2.50e+03 pdb=" C2 U E 53 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U E 53 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U E 53 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U E 53 " 0.006 2.00e-02 2.50e+03 pdb=" O4 U E 53 " 0.012 2.00e-02 2.50e+03 pdb=" C5 U E 53 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U E 53 " -0.014 2.00e-02 2.50e+03 ... (remaining 742 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2668 2.90 - 3.40: 6478 3.40 - 3.90: 14648 3.90 - 4.40: 15866 4.40 - 4.90: 21804 Nonbonded interactions: 61464 Sorted by model distance: nonbonded pdb=" N4 DC C 11 " pdb=" N6 A E 159 " model vdw 2.401 2.560 nonbonded pdb=" O5' A E 8 " pdb=" O4' A E 8 " model vdw 2.468 2.432 nonbonded pdb=" O5' A E 52 " pdb=" O4' A E 52 " model vdw 2.480 2.432 nonbonded pdb=" O5' C E 92 " pdb=" O4' C E 92 " model vdw 2.482 2.432 nonbonded pdb=" O5' A E 100 " pdb=" O4' A E 100 " model vdw 2.488 2.432 ... (remaining 61459 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 194) 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.400 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 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 : 0.006 0.055 7948 Z= 0.470 Angle : 1.139 10.596 11655 Z= 0.955 Chirality : 0.058 0.302 1432 Planarity : 0.007 0.049 745 Dihedral : 26.656 173.682 4122 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.28 % Allowed : 33.61 % Favored : 66.11 % 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: 0.04 (0.42), residues: 385 helix: 1.60 (0.41), residues: 153 sheet: -1.08 (0.59), residues: 71 loop : -0.94 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 24 TYR 0.025 0.003 TYR B 45 PHE 0.014 0.002 PHE A 179 TRP 0.010 0.003 TRP B 137 HIS 0.006 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.47 ( 7948) covalent geometry : angle 1.13907 / 0.96 (11655) hydrogen bonds : bond 0.12761 / 8.30 ( 304) hydrogen bonds : angle 5.68195 / 4.03 ( 749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0877 time to fit residues: 12.5629 Evaluate side-chains 71 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 183 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 139 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.102844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.075441 restraints weight = 27612.262| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.83 r_work: 0.3291 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7948 Z= 0.223 Angle : 0.736 9.225 11655 Z= 0.432 Chirality : 0.047 0.297 1432 Planarity : 0.005 0.034 745 Dihedral : 26.825 178.429 3300 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.16 % Allowed : 33.05 % Favored : 60.78 % 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: 0.41 (0.42), residues: 385 helix: 1.90 (0.40), residues: 152 sheet: -0.74 (0.63), residues: 71 loop : -0.79 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 159 TYR 0.043 0.003 TYR B 20 PHE 0.011 0.002 PHE A 143 TRP 0.003 0.001 TRP A 137 HIS 0.007 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 ( 7948) covalent geometry : angle 0.73586 / 0.43 (11655) hydrogen bonds : bond 0.07320 / 4.82 ( 304) hydrogen bonds : angle 4.21415 / 3.08 ( 749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8612 (mp0) cc_final: 0.8246 (mp0) REVERT: A 106 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7706 (ttm110) REVERT: A 183 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7652 (t0) REVERT: B 18 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8738 (pm20) REVERT: B 20 TYR cc_start: 0.8934 (m-80) cc_final: 0.8506 (m-80) outliers start: 22 outliers final: 10 residues processed: 85 average time/residue: 0.0620 time to fit residues: 7.4611 Evaluate side-chains 71 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 10.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.102307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.074835 restraints weight = 27428.353| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.79 r_work: 0.3279 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7948 Z= 0.190 Angle : 0.641 7.068 11655 Z= 0.387 Chirality : 0.042 0.270 1432 Planarity : 0.004 0.039 745 Dihedral : 26.458 179.334 3300 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.88 % Allowed : 31.65 % Favored : 62.46 % 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: 0.61 (0.43), residues: 385 helix: 2.12 (0.41), residues: 152 sheet: -0.52 (0.66), residues: 72 loop : -0.82 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 184 TYR 0.018 0.002 TYR B 20 PHE 0.015 0.002 PHE B 161 TRP 0.003 0.001 TRP B 137 HIS 0.005 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 ( 7948) covalent geometry : angle 0.64075 / 0.39 (11655) hydrogen bonds : bond 0.06425 / 4.18 ( 304) hydrogen bonds : angle 3.80582 / 2.81 ( 749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8660 (mp0) cc_final: 0.8202 (mp0) REVERT: A 183 ASN cc_start: 0.8457 (t0) cc_final: 0.8096 (t0) REVERT: A 187 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8170 (tp) REVERT: B 20 TYR cc_start: 0.9100 (m-80) cc_final: 0.8851 (m-80) REVERT: B 102 GLU cc_start: 0.8131 (mp0) cc_final: 0.7809 (mp0) outliers start: 21 outliers final: 10 residues processed: 80 average time/residue: 0.0767 time to fit residues: 8.4291 Evaluate side-chains 68 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.101986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.074544 restraints weight = 28096.431| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.88 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7948 Z= 0.165 Angle : 0.587 7.006 11655 Z= 0.351 Chirality : 0.039 0.267 1432 Planarity : 0.003 0.024 745 Dihedral : 26.205 177.951 3300 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.04 % Allowed : 29.97 % Favored : 64.99 % 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: 0.53 (0.43), residues: 385 helix: 2.21 (0.41), residues: 153 sheet: -0.43 (0.68), residues: 66 loop : -1.12 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 117 TYR 0.021 0.002 TYR B 45 PHE 0.020 0.002 PHE B 123 TRP 0.005 0.001 TRP B 137 HIS 0.005 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 ( 7948) covalent geometry : angle 0.58711 / 0.35 (11655) hydrogen bonds : bond 0.06040 / 3.97 ( 304) hydrogen bonds : angle 3.61213 / 2.62 ( 749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8421 (mp0) cc_final: 0.7904 (mp0) REVERT: A 104 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8564 (t) REVERT: A 187 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7545 (tp) REVERT: B 18 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: B 64 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8730 (t0) REVERT: B 102 GLU cc_start: 0.7940 (mp0) cc_final: 0.7683 (mp0) REVERT: B 189 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6266 (tt) outliers start: 18 outliers final: 10 residues processed: 73 average time/residue: 0.0649 time to fit residues: 6.5589 Evaluate side-chains 70 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.099712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071611 restraints weight = 27357.811| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.80 r_work: 0.3198 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7948 Z= 0.220 Angle : 0.656 7.767 11655 Z= 0.387 Chirality : 0.043 0.300 1432 Planarity : 0.005 0.071 745 Dihedral : 26.076 175.273 3300 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.84 % Allowed : 27.73 % Favored : 64.43 % 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: 0.21 (0.43), residues: 385 helix: 1.70 (0.41), residues: 153 sheet: -0.63 (0.64), residues: 69 loop : -1.00 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 16 TYR 0.023 0.003 TYR B 108 PHE 0.020 0.002 PHE B 143 TRP 0.005 0.001 TRP B 137 HIS 0.012 0.003 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 ( 7948) covalent geometry : angle 0.65591 / 0.39 (11655) hydrogen bonds : bond 0.06729 / 4.33 ( 304) hydrogen bonds : angle 3.79908 / 2.76 ( 749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8924 (mp0) cc_final: 0.8405 (mp0) REVERT: A 27 MET cc_start: 0.8458 (ttt) cc_final: 0.8142 (ttm) REVERT: A 102 GLU cc_start: 0.8728 (mp0) cc_final: 0.8438 (mp0) REVERT: A 104 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8892 (t) REVERT: A 186 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8266 (mt) REVERT: A 187 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8211 (tp) REVERT: B 18 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8866 (pm20) REVERT: B 64 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8792 (t0) outliers start: 28 outliers final: 13 residues processed: 74 average time/residue: 0.0722 time to fit residues: 7.2730 Evaluate side-chains 66 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 194 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.098038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069843 restraints weight = 27619.796| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.83 r_work: 0.3162 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7948 Z= 0.246 Angle : 0.635 7.598 11655 Z= 0.372 Chirality : 0.041 0.277 1432 Planarity : 0.004 0.036 745 Dihedral : 26.109 177.332 3300 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.44 % Allowed : 27.73 % Favored : 65.83 % 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: 0.36 (0.43), residues: 385 helix: 2.05 (0.41), residues: 153 sheet: -0.64 (0.64), residues: 74 loop : -1.13 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 110 TYR 0.020 0.002 TYR A 125 PHE 0.017 0.002 PHE B 161 TRP 0.004 0.001 TRP B 137 HIS 0.008 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 ( 7948) covalent geometry : angle 0.63524 / 0.37 (11655) hydrogen bonds : bond 0.06556 / 4.28 ( 304) hydrogen bonds : angle 3.71364 / 2.68 ( 749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8996 (mp0) cc_final: 0.8503 (mp0) REVERT: A 27 MET cc_start: 0.8502 (ttt) cc_final: 0.8280 (ttm) REVERT: A 104 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8942 (t) REVERT: A 186 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8368 (mt) REVERT: A 187 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8133 (tp) REVERT: B 18 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8831 (pm20) REVERT: B 64 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.8776 (t0) REVERT: B 100 LYS cc_start: 0.9111 (ttpt) cc_final: 0.8749 (ttpp) REVERT: B 189 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7153 (tt) outliers start: 23 outliers final: 9 residues processed: 63 average time/residue: 0.0743 time to fit residues: 6.4735 Evaluate side-chains 59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 10.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.100214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072310 restraints weight = 28348.690| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.86 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7948 Z= 0.135 Angle : 0.553 7.138 11655 Z= 0.329 Chirality : 0.038 0.251 1432 Planarity : 0.004 0.047 745 Dihedral : 25.999 179.665 3300 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.76 % Allowed : 30.25 % Favored : 64.99 % 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: 0.61 (0.44), residues: 385 helix: 2.13 (0.41), residues: 154 sheet: -0.20 (0.68), residues: 64 loop : -1.01 (0.48), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 164 TYR 0.018 0.002 TYR B 108 PHE 0.016 0.001 PHE B 161 TRP 0.007 0.001 TRP B 137 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 ( 7948) covalent geometry : angle 0.55326 / 0.33 (11655) hydrogen bonds : bond 0.05481 / 3.53 ( 304) hydrogen bonds : angle 3.41091 / 2.44 ( 749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8706 (mp0) cc_final: 0.8135 (mp0) REVERT: A 27 MET cc_start: 0.8281 (ttt) cc_final: 0.8070 (ttm) REVERT: B 18 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8695 (pm20) REVERT: B 64 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.8715 (t0) REVERT: B 100 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8642 (ttpp) REVERT: B 189 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6865 (tt) outliers start: 17 outliers final: 12 residues processed: 62 average time/residue: 0.0839 time to fit residues: 7.1223 Evaluate side-chains 59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 0.0870 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.100910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.072369 restraints weight = 27771.546| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.87 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7948 Z= 0.137 Angle : 0.543 7.415 11655 Z= 0.321 Chirality : 0.037 0.253 1432 Planarity : 0.003 0.030 745 Dihedral : 25.865 177.838 3300 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.92 % Allowed : 31.37 % Favored : 64.71 % 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: 0.79 (0.44), residues: 385 helix: 2.23 (0.41), residues: 155 sheet: 0.01 (0.69), residues: 64 loop : -0.93 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 110 TYR 0.019 0.002 TYR A 125 PHE 0.019 0.001 PHE B 161 TRP 0.005 0.001 TRP B 137 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 ( 7948) covalent geometry : angle 0.54337 / 0.32 (11655) hydrogen bonds : bond 0.05479 / 3.53 ( 304) hydrogen bonds : angle 3.26402 / 2.33 ( 749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.192 Fit side-chains REVERT: A 18 GLU cc_start: 0.8770 (mp0) cc_final: 0.8201 (mp0) REVERT: A 109 LYS cc_start: 0.8365 (mptt) cc_final: 0.8116 (mptt) REVERT: B 18 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8746 (pm20) REVERT: B 64 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8561 (t0) REVERT: B 100 LYS cc_start: 0.9022 (ttpt) cc_final: 0.8575 (ttpp) REVERT: B 189 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6639 (tt) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 0.0867 time to fit residues: 7.0785 Evaluate side-chains 58 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.101499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.073654 restraints weight = 27144.347| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.78 r_work: 0.3361 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.7069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7948 Z= 0.128 Angle : 0.532 7.030 11655 Z= 0.316 Chirality : 0.036 0.246 1432 Planarity : 0.003 0.035 745 Dihedral : 25.818 177.588 3300 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 32.49 % Favored : 64.43 % 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: 0.81 (0.44), residues: 385 helix: 2.19 (0.40), residues: 155 sheet: 0.01 (0.70), residues: 64 loop : -0.87 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 110 TYR 0.017 0.002 TYR A 125 PHE 0.019 0.001 PHE B 161 TRP 0.005 0.001 TRP B 137 HIS 0.001 0.000 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 ( 7948) covalent geometry : angle 0.53204 / 0.32 (11655) hydrogen bonds : bond 0.05189 / 3.34 ( 304) hydrogen bonds : angle 3.22038 / 2.30 ( 749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.9007 (mp0) cc_final: 0.8483 (mp0) REVERT: A 102 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8231 (mt-10) REVERT: B 18 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8736 (pm20) REVERT: B 64 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8507 (t0) REVERT: B 100 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8633 (ttpp) REVERT: B 189 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6942 (tt) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0885 time to fit residues: 7.3566 Evaluate side-chains 58 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.099684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.071815 restraints weight = 27272.410| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.75 r_work: 0.3317 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7948 Z= 0.177 Angle : 0.553 7.158 11655 Z= 0.328 Chirality : 0.037 0.260 1432 Planarity : 0.004 0.027 745 Dihedral : 25.772 177.215 3300 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.92 % Allowed : 31.65 % Favored : 64.43 % 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: 0.86 (0.44), residues: 385 helix: 2.34 (0.41), residues: 155 sheet: 0.01 (0.69), residues: 64 loop : -0.94 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 110 TYR 0.017 0.002 TYR A 125 PHE 0.023 0.001 PHE B 161 TRP 0.003 0.001 TRP B 137 HIS 0.001 0.001 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 ( 7948) covalent geometry : angle 0.55332 / 0.33 (11655) hydrogen bonds : bond 0.05667 / 3.66 ( 304) hydrogen bonds : angle 3.31311 / 2.38 ( 749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7953 (mmm-85) REVERT: A 18 GLU cc_start: 0.9036 (mp0) cc_final: 0.8520 (mp0) REVERT: B 18 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8756 (pm20) REVERT: B 64 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8543 (t0) REVERT: B 100 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8712 (ttpp) REVERT: B 189 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7061 (tt) outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.0946 time to fit residues: 7.2567 Evaluate side-chains 57 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.100095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.072013 restraints weight = 27081.341| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.83 r_work: 0.3331 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7948 Z= 0.155 Angle : 0.550 8.744 11655 Z= 0.324 Chirality : 0.037 0.251 1432 Planarity : 0.004 0.031 745 Dihedral : 25.740 176.948 3300 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.48 % Allowed : 30.81 % Favored : 64.71 % 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: 0.83 (0.44), residues: 385 helix: 2.26 (0.41), residues: 155 sheet: 0.07 (0.68), residues: 64 loop : -0.93 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.017 0.002 TYR B 170 PHE 0.024 0.001 PHE B 161 TRP 0.003 0.001 TRP B 137 HIS 0.001 0.001 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 ( 7948) covalent geometry : angle 0.54983 / 0.32 (11655) hydrogen bonds : bond 0.05320 / 3.45 ( 304) hydrogen bonds : angle 3.25768 / 2.34 ( 749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1765.83 seconds wall clock time: 31 minutes 4.89 seconds (1864.89 seconds total)