Starting phenix.real_space_refine on Tue Aug 4 23:32:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzp_49955/08_2026/9nzp_49955.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzp_49955/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nzp_49955/08_2026/9nzp_49955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzp_49955/08_2026/9nzp_49955.map" model { file = "/net/cci-nas-00/data/ceres_data/9nzp_49955/08_2026/9nzp_49955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzp_49955/08_2026/9nzp_49955.cif" } 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-2.2rc3-6140/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: 1.70, per 1000 atoms: 0.23 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: 0.50 Conformation dependent library (CDL) restraints added in 337.2 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: 1.03 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: 1.08 Time building geometry restraints manager: 0.71 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: 10572 2.12 - 4.24: 955 4.24 - 6.36: 86 6.36 - 8.48: 33 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=" O5' A E 137 " pdb=" C5' A E 137 " pdb=" C4' A E 137 " ideal model delta sigma weight residual 109.40 115.10 -5.70 8.00e-01 1.56e+00 5.09e+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=" O5' G E 68 " pdb=" C5' G E 68 " pdb=" C4' G E 68 " ideal model delta sigma weight residual 109.40 114.63 -5.23 8.00e-01 1.56e+00 4.27e+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: 946 0.060 - 0.121: 302 0.121 - 0.181: 161 0.181 - 0.242: 17 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 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= 0.498 Angle : 1.240 10.596 11655 Z= 1.067 Chirality : 0.072 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 0.00628 / 0.50 ( 7948) covalent geometry : angle 1.23991 / 1.07 (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 : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0787 time to fit residues: 11.4846 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 : 0.106 ------------------------------------------------------------------------------- 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: 30.0000 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 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: 3.9990 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 89 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.102995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.075360 restraints weight = 28242.598| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.86 r_work: 0.3270 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 7948 Z= 0.224 Angle : 0.824 9.615 11655 Z= 0.445 Chirality : 0.054 0.486 1432 Planarity : 0.005 0.041 745 Dihedral : 26.655 179.779 3300 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 7.28 % Allowed : 32.21 % Favored : 60.50 % 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: 0.38 (0.42), residues: 385 helix: 1.87 (0.41), residues: 152 sheet: -0.71 (0.64), residues: 71 loop : -0.84 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 159 TYR 0.027 0.003 TYR B 20 PHE 0.012 0.002 PHE A 143 TRP 0.003 0.001 TRP A 137 HIS 0.006 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.22 ( 7948) covalent geometry : angle 0.82369 / 0.45 (11655) hydrogen bonds : bond 0.07214 / 4.75 ( 304) hydrogen bonds : angle 4.18394 / 3.06 ( 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 94 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8686 (mp0) cc_final: 0.8313 (mp0) REVERT: A 183 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7702 (t0) REVERT: B 18 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8763 (pm20) REVERT: B 20 TYR cc_start: 0.9013 (m-80) cc_final: 0.8604 (m-80) outliers start: 26 outliers final: 12 residues processed: 91 average time/residue: 0.0699 time to fit residues: 8.8608 Evaluate side-chains 72 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 194 THR 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: 0.6980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 10.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 40.0000 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.102121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074413 restraints weight = 27313.804| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.80 r_work: 0.3281 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7948 Z= 0.185 Angle : 0.684 8.472 11655 Z= 0.388 Chirality : 0.045 0.463 1432 Planarity : 0.004 0.026 745 Dihedral : 26.336 179.532 3300 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.04 % Allowed : 32.49 % 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: 0.47 (0.43), residues: 385 helix: 2.06 (0.41), residues: 152 sheet: -0.59 (0.64), residues: 75 loop : -0.95 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 184 TYR 0.017 0.002 TYR A 125 PHE 0.014 0.002 PHE B 161 TRP 0.006 0.001 TRP B 137 HIS 0.003 0.001 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 ( 7948) covalent geometry : angle 0.68394 / 0.39 (11655) hydrogen bonds : bond 0.06572 / 4.30 ( 304) hydrogen bonds : angle 3.79531 / 2.79 ( 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 79 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8656 (mp0) cc_final: 0.8181 (mp0) REVERT: A 187 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8197 (tp) REVERT: B 20 TYR cc_start: 0.9125 (m-80) cc_final: 0.8872 (m-80) REVERT: B 102 GLU cc_start: 0.8083 (mp0) cc_final: 0.7819 (mp0) outliers start: 18 outliers final: 10 residues processed: 75 average time/residue: 0.0772 time to fit residues: 7.9369 Evaluate side-chains 67 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 41 LEU 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 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: 2.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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 = 0.4074 r_free = 0.4074 target = 0.101462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.073981 restraints weight = 28051.363| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.90 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7948 Z= 0.174 Angle : 0.638 9.512 11655 Z= 0.359 Chirality : 0.044 0.474 1432 Planarity : 0.004 0.039 745 Dihedral : 26.043 178.618 3300 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.44 % Allowed : 26.89 % Favored : 66.67 % 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: 0.44 (0.43), residues: 385 helix: 2.18 (0.41), residues: 153 sheet: -0.63 (0.66), residues: 66 loop : -1.13 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 5 TYR 0.029 0.002 TYR B 45 PHE 0.016 0.002 PHE B 143 TRP 0.018 0.002 TRP B 137 HIS 0.007 0.002 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 7948) covalent geometry : angle 0.63804 / 0.36 (11655) hydrogen bonds : bond 0.06044 / 4.00 ( 304) hydrogen bonds : angle 3.72363 / 2.72 ( 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 84 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8483 (mp0) cc_final: 0.7930 (mp0) REVERT: A 104 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8575 (t) REVERT: A 150 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8290 (mm-30) REVERT: A 187 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7382 (tp) REVERT: B 18 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8701 (pm20) REVERT: B 64 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8743 (t0) REVERT: B 102 GLU cc_start: 0.7967 (mp0) cc_final: 0.7414 (mp0) outliers start: 23 outliers final: 12 residues processed: 77 average time/residue: 0.0807 time to fit residues: 8.2986 Evaluate side-chains 71 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 114 LEU 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 185 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 49 optimal weight: 40.0000 chunk 46 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.101046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073498 restraints weight = 27619.532| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.83 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7948 Z= 0.169 Angle : 0.590 7.665 11655 Z= 0.338 Chirality : 0.041 0.445 1432 Planarity : 0.004 0.050 745 Dihedral : 25.858 176.542 3300 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.60 % Allowed : 28.01 % Favored : 66.39 % 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: 0.47 (0.43), residues: 385 helix: 2.13 (0.41), residues: 153 sheet: -0.62 (0.64), residues: 72 loop : -1.05 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 24 TYR 0.020 0.002 TYR A 125 PHE 0.017 0.002 PHE B 143 TRP 0.006 0.002 TRP B 137 HIS 0.005 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 7948) covalent geometry : angle 0.59046 / 0.34 (11655) hydrogen bonds : bond 0.05944 / 3.83 ( 304) hydrogen bonds : angle 3.55770 / 2.61 ( 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 75 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8560 (mp0) cc_final: 0.7961 (mp0) REVERT: A 27 MET cc_start: 0.8219 (ttt) cc_final: 0.8005 (ttm) REVERT: A 102 GLU cc_start: 0.8211 (mp0) cc_final: 0.7817 (mp0) REVERT: A 104 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8634 (t) REVERT: A 109 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7938 (mmtm) REVERT: A 187 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7704 (tp) REVERT: A 191 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8805 (m) REVERT: B 18 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8790 (pm20) REVERT: B 64 ASN cc_start: 0.9239 (OUTLIER) cc_final: 0.8764 (t0) REVERT: B 102 GLU cc_start: 0.8084 (mp0) cc_final: 0.7769 (mp0) outliers start: 20 outliers final: 10 residues processed: 71 average time/residue: 0.0712 time to fit residues: 6.9249 Evaluate side-chains 67 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 9 ILE 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 141 ILE Chi-restraints excluded: chain B residue 181 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 54 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 28 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.101216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.073735 restraints weight = 27635.554| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.77 r_work: 0.3252 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5688 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= 0.147 Angle : 0.558 7.288 11655 Z= 0.321 Chirality : 0.040 0.462 1432 Planarity : 0.003 0.027 745 Dihedral : 25.758 179.572 3300 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.60 % Allowed : 28.01 % Favored : 66.39 % 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: 0.50 (0.43), residues: 385 helix: 2.14 (0.41), residues: 153 sheet: -0.54 (0.64), residues: 72 loop : -1.06 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 110 TYR 0.018 0.002 TYR B 45 PHE 0.011 0.001 PHE A 161 TRP 0.006 0.001 TRP B 137 HIS 0.001 0.000 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 ( 7948) covalent geometry : angle 0.55778 / 0.32 (11655) hydrogen bonds : bond 0.05659 / 3.69 ( 304) hydrogen bonds : angle 3.51133 / 2.55 ( 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 74 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8932 (mp0) cc_final: 0.8408 (mp0) REVERT: A 27 MET cc_start: 0.8469 (ttt) cc_final: 0.8216 (ttm) REVERT: A 104 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8865 (t) REVERT: A 109 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8221 (mmtm) REVERT: A 187 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7852 (tp) REVERT: A 191 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.9001 (m) REVERT: B 18 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8794 (pm20) REVERT: B 64 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8774 (t0) REVERT: B 100 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8208 (ptmm) REVERT: B 189 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6571 (tt) outliers start: 20 outliers final: 9 residues processed: 69 average time/residue: 0.0806 time to fit residues: 7.4728 Evaluate side-chains 66 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 133 VAL 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 105 ILE 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=2.50 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.102652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.074612 restraints weight = 27652.048| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.86 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7948 Z= 0.131 Angle : 0.546 7.538 11655 Z= 0.312 Chirality : 0.039 0.440 1432 Planarity : 0.003 0.032 745 Dihedral : 25.644 178.697 3300 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.36 % Allowed : 29.69 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.43), residues: 385 helix: 2.26 (0.41), residues: 153 sheet: -0.24 (0.66), residues: 72 loop : -1.02 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 5 TYR 0.017 0.002 TYR B 45 PHE 0.012 0.001 PHE B 161 TRP 0.002 0.001 TRP B 137 HIS 0.001 0.000 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 7948) covalent geometry : angle 0.54557 / 0.31 (11655) hydrogen bonds : bond 0.05405 / 3.46 ( 304) hydrogen bonds : angle 3.32090 / 2.38 ( 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 63 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8701 (mp0) cc_final: 0.8091 (mp0) REVERT: A 27 MET cc_start: 0.8121 (ttt) cc_final: 0.7881 (ttm) REVERT: A 109 LYS cc_start: 0.8208 (mmtm) cc_final: 0.7941 (mmtm) REVERT: A 150 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 189 LEU cc_start: 0.9075 (tp) cc_final: 0.8863 (tt) REVERT: B 18 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8816 (pm20) REVERT: B 64 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8625 (t0) REVERT: B 100 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8063 (ptmm) REVERT: B 189 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6072 (tt) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 0.0660 time to fit residues: 5.6403 Evaluate side-chains 59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 133 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 105 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 46 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 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 = 0.4142 r_free = 0.4142 target = 0.102904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.074941 restraints weight = 27227.853| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.83 r_work: 0.3409 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7948 Z= 0.125 Angle : 0.529 7.350 11655 Z= 0.305 Chirality : 0.038 0.453 1432 Planarity : 0.003 0.025 745 Dihedral : 25.575 177.819 3300 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.92 % Allowed : 30.25 % 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: 0.67 (0.44), residues: 385 helix: 2.18 (0.41), residues: 153 sheet: -0.16 (0.67), residues: 72 loop : -0.99 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.017 0.002 TYR B 45 PHE 0.012 0.001 PHE B 161 TRP 0.003 0.001 TRP A 137 HIS 0.003 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 ( 7948) covalent geometry : angle 0.52890 / 0.31 (11655) hydrogen bonds : bond 0.05345 / 3.44 ( 304) hydrogen bonds : angle 3.27453 / 2.35 ( 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 65 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8939 (mp0) cc_final: 0.8365 (mp0) REVERT: A 27 MET cc_start: 0.8263 (ttt) cc_final: 0.8059 (ttm) REVERT: A 109 LYS cc_start: 0.8349 (mmtm) cc_final: 0.8115 (mmtm) REVERT: A 150 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8370 (mm-30) REVERT: B 18 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8830 (pm20) REVERT: B 64 ASN cc_start: 0.9224 (OUTLIER) cc_final: 0.8566 (t0) REVERT: B 100 LYS cc_start: 0.8965 (ttpt) cc_final: 0.8117 (ptmm) REVERT: B 189 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6340 (tt) outliers start: 14 outliers final: 8 residues processed: 63 average time/residue: 0.0761 time to fit residues: 6.5522 Evaluate side-chains 60 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 126 CYS Chi-restraints excluded: chain A residue 133 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 141 ILE 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: 0.0040 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 47 optimal weight: 9.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.104621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077214 restraints weight = 29742.935| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.89 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7948 Z= 0.115 Angle : 0.535 10.467 11655 Z= 0.302 Chirality : 0.038 0.434 1432 Planarity : 0.003 0.025 745 Dihedral : 25.542 177.432 3300 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.36 % Allowed : 31.37 % Favored : 65.27 % 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: 0.74 (0.44), residues: 385 helix: 2.19 (0.41), residues: 153 sheet: 0.03 (0.68), residues: 72 loop : -1.00 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.017 0.002 TYR B 45 PHE 0.016 0.001 PHE B 161 TRP 0.004 0.000 TRP A 137 HIS 0.001 0.000 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.12 ( 7948) covalent geometry : angle 0.53480 / 0.30 (11655) hydrogen bonds : bond 0.05161 / 3.29 ( 304) hydrogen bonds : angle 3.18614 / 2.27 ( 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 64 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8734 (mp0) cc_final: 0.8519 (mp0) REVERT: A 27 MET cc_start: 0.8180 (ttt) cc_final: 0.7941 (ttm) REVERT: A 38 MET cc_start: 0.9048 (tpt) cc_final: 0.8833 (tpp) REVERT: A 109 LYS cc_start: 0.8272 (mmtm) cc_final: 0.8030 (mmtm) REVERT: A 150 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 18 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8774 (pm20) REVERT: B 64 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8632 (t0) REVERT: B 189 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6142 (tt) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.0813 time to fit residues: 6.7971 Evaluate side-chains 59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 126 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 64 ASN 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: 4.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.102183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.074136 restraints weight = 27767.706| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.84 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7948 Z= 0.144 Angle : 0.535 7.766 11655 Z= 0.307 Chirality : 0.039 0.457 1432 Planarity : 0.003 0.025 745 Dihedral : 25.496 176.915 3300 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.36 % Allowed : 31.93 % 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: 0.65 (0.44), residues: 385 helix: 2.16 (0.41), residues: 153 sheet: -0.07 (0.67), residues: 72 loop : -1.06 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 110 TYR 0.016 0.002 TYR B 45 PHE 0.015 0.002 PHE B 161 TRP 0.013 0.002 TRP B 137 HIS 0.001 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 7948) covalent geometry : angle 0.53462 / 0.31 (11655) hydrogen bonds : bond 0.05440 / 3.51 ( 304) hydrogen bonds : angle 3.27702 / 2.35 ( 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 60 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8760 (mp0) cc_final: 0.8145 (mp0) REVERT: A 27 MET cc_start: 0.8231 (ttt) cc_final: 0.8011 (ttm) REVERT: A 109 LYS cc_start: 0.8340 (mmtm) cc_final: 0.8081 (mmtm) REVERT: A 150 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 18 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8768 (pm20) REVERT: B 64 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8654 (t0) REVERT: B 100 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8561 (ttpp) REVERT: B 189 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6371 (tt) outliers start: 12 outliers final: 9 residues processed: 58 average time/residue: 0.0731 time to fit residues: 5.7790 Evaluate side-chains 59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 55 GLU 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 18 GLU Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 102 GLU 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: 4.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 40.0000 chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.101265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.073412 restraints weight = 29591.679| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.89 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.7312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7948 Z= 0.175 Angle : 0.589 12.959 11655 Z= 0.326 Chirality : 0.040 0.450 1432 Planarity : 0.004 0.025 745 Dihedral : 25.554 176.525 3300 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.20 % Allowed : 31.09 % 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: 0.70 (0.44), residues: 385 helix: 2.18 (0.41), residues: 154 sheet: -0.05 (0.71), residues: 67 loop : -1.00 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 110 TYR 0.018 0.002 TYR B 45 PHE 0.016 0.002 PHE B 161 TRP 0.002 0.001 TRP A 137 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 ( 7948) covalent geometry : angle 0.58870 / 0.33 (11655) hydrogen bonds : bond 0.05467 / 3.50 ( 304) hydrogen bonds : angle 3.37441 / 2.43 ( 749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.86 seconds wall clock time: 25 minutes 59.40 seconds (1559.40 seconds total)