Starting phenix.real_space_refine on Thu Aug 6 06:02:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qv6_53387/08_2026/9qv6_53387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qv6_53387/08_2026/9qv6_53387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qv6_53387/08_2026/9qv6_53387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qv6_53387/08_2026/9qv6_53387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qv6_53387/08_2026/9qv6_53387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qv6_53387/08_2026/9qv6_53387.map" } resolution = 2.6 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= 0.008 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 360 5.49 5 S 24 5.16 5 C 7516 2.51 5 N 2636 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s 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: 13932 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "F" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "H" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "I" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "J" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "K" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "L" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'TRANS': 70} Chain: "X" Number of atoms: 3674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3674 Classifications: {'DNA': 180} Link IDs: {'rna3p': 179} Chain: "Y" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3706 Classifications: {'DNA': 180} Link IDs: {'rna3p': 179} Time building chain proxies: 2.71, per 1000 atoms: 0.19 Number of scatterers: 13932 At special positions: 0 Unit cell: (114.165, 114.165, 93.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 360 15.00 O 3396 8.00 N 2636 7.00 C 7516 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: 0.82 Conformation dependent library (CDL) restraints added in 361.4 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 74.6% alpha, 2.8% beta 100 base pairs and 300 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 23 through 53 Processing helix chain 'B' and resid 58 through 67 Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 23 through 53 Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'D' and resid 6 through 17 Processing helix chain 'D' and resid 23 through 53 Processing helix chain 'D' and resid 58 through 67 Processing helix chain 'E' and resid 6 through 17 Processing helix chain 'E' and resid 23 through 53 Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'F' and resid 6 through 17 Processing helix chain 'F' and resid 23 through 53 Processing helix chain 'F' and resid 58 through 67 Processing helix chain 'G' and resid 6 through 17 Processing helix chain 'G' and resid 23 through 53 Processing helix chain 'G' and resid 58 through 67 Processing helix chain 'H' and resid 6 through 17 Processing helix chain 'H' and resid 23 through 53 Processing helix chain 'H' and resid 58 through 67 Processing helix chain 'I' and resid 6 through 17 Processing helix chain 'I' and resid 23 through 53 Processing helix chain 'I' and resid 58 through 67 Processing helix chain 'J' and resid 6 through 17 Processing helix chain 'J' and resid 23 through 53 Processing helix chain 'J' and resid 58 through 67 Processing helix chain 'K' and resid 6 through 17 Processing helix chain 'K' and resid 23 through 53 Processing helix chain 'K' and resid 58 through 67 Processing helix chain 'L' and resid 6 through 17 Processing helix chain 'L' and resid 23 through 53 Processing helix chain 'L' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 7.080A pdb=" N ARG A 21 " --> pdb=" O VAL B 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 22 removed outlier: 7.034A pdb=" N ARG C 21 " --> pdb=" O VAL D 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 22 removed outlier: 7.101A pdb=" N ARG E 21 " --> pdb=" O VAL F 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'G' and resid 21 through 22 removed outlier: 7.144A pdb=" N ARG G 21 " --> pdb=" O VAL H 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57 Processing sheet with id=AA9, first strand: chain 'I' and resid 21 through 22 removed outlier: 7.132A pdb=" N ARG I 21 " --> pdb=" O VAL J 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'I' and resid 56 through 57 Processing sheet with id=AB2, first strand: chain 'K' and resid 21 through 22 removed outlier: 7.110A pdb=" N ARG K 21 " --> pdb=" O VAL L 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 56 through 57 498 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 233 hydrogen bonds 466 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 300 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1850 1.32 - 1.44: 5034 1.44 - 1.56: 7228 1.56 - 1.69: 718 1.69 - 1.81: 48 Bond restraints: 14878 Sorted by residual: bond pdb=" C ARG J 9 " pdb=" O ARG J 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.17e+01 bond pdb=" C ARG B 9 " pdb=" O ARG B 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.17e+01 bond pdb=" C ARG L 9 " pdb=" O ARG L 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" C ARG A 9 " pdb=" O ARG A 9 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.16e+01 bond pdb=" C ARG F 9 " pdb=" O ARG F 9 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.28e-02 6.10e+03 1.15e+01 ... (remaining 14873 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 15160 1.65 - 3.29: 4284 3.29 - 4.94: 1452 4.94 - 6.58: 654 6.58 - 8.23: 54 Bond angle restraints: 21604 Sorted by residual: angle pdb=" O4' DT Y 91 " pdb=" C4' DT Y 91 " pdb=" C3' DT Y 91 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" C3' DT Y 91 " pdb=" O3' DT Y 91 " pdb=" P DA Y 92 " ideal model delta sigma weight residual 119.70 125.41 -5.71 1.20e+00 6.94e-01 2.27e+01 angle pdb=" C4' DG X 99 " pdb=" O4' DG X 99 " pdb=" C1' DG X 99 " ideal model delta sigma weight residual 110.10 105.85 4.25 1.00e+00 1.00e+00 1.81e+01 angle pdb=" O4' DT X 38 " pdb=" C4' DT X 38 " pdb=" C3' DT X 38 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" O4' DT X 162 " pdb=" C4' DT X 162 " pdb=" C3' DT X 162 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 21599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 6300 35.07 - 70.13: 1686 70.13 - 105.20: 36 105.20 - 140.27: 0 140.27 - 175.34: 4 Dihedral angle restraints: 8026 sinusoidal: 5566 harmonic: 2460 Sorted by residual: dihedral pdb=" CD ARG L 9 " pdb=" NE ARG L 9 " pdb=" CZ ARG L 9 " pdb=" NH1 ARG L 9 " ideal model delta sinusoidal sigma weight residual 0.00 52.69 -52.69 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CD ARG I 9 " pdb=" NE ARG I 9 " pdb=" CZ ARG I 9 " pdb=" NH1 ARG I 9 " ideal model delta sinusoidal sigma weight residual 0.00 52.67 -52.67 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CD ARG D 9 " pdb=" NE ARG D 9 " pdb=" CZ ARG D 9 " pdb=" NH1 ARG D 9 " ideal model delta sinusoidal sigma weight residual 0.00 52.67 -52.67 1 1.00e+01 1.00e-02 3.78e+01 ... (remaining 8023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1988 0.127 - 0.255: 76 0.255 - 0.382: 15 0.382 - 0.510: 220 0.510 - 0.637: 125 Chirality restraints: 2424 Sorted by residual: chirality pdb=" P DC Y 1 " pdb=" OP1 DC Y 1 " pdb=" OP2 DC Y 1 " pdb=" O5' DC Y 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DA Y 92 " pdb=" OP1 DA Y 92 " pdb=" OP2 DA Y 92 " pdb=" O5' DA Y 92 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.74e+00 chirality pdb=" P DC X 1 " pdb=" OP1 DC X 1 " pdb=" OP2 DC X 1 " pdb=" O5' DC X 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.67e+00 ... (remaining 2421 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 9 " -0.879 9.50e-02 1.11e+02 3.94e-01 9.43e+01 pdb=" NE ARG B 9 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B 9 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 9 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 9 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 9 " -0.879 9.50e-02 1.11e+02 3.94e-01 9.43e+01 pdb=" NE ARG D 9 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG D 9 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 9 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 9 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 9 " 0.879 9.50e-02 1.11e+02 3.94e-01 9.42e+01 pdb=" NE ARG E 9 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG E 9 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 9 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 9 " 0.025 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5549 3.00 - 3.47: 14403 3.47 - 3.95: 27242 3.95 - 4.42: 31292 4.42 - 4.90: 41244 Nonbonded interactions: 119730 Sorted by model distance: nonbonded pdb=" O4' DC X 157 " pdb=" O2 DC X 157 " model vdw 2.525 3.040 nonbonded pdb=" O5' DG X 150 " pdb=" O4' DG X 150 " model vdw 2.558 2.432 nonbonded pdb=" O5' DG X 161 " pdb=" O4' DG X 161 " model vdw 2.589 2.432 nonbonded pdb=" N1 DG X 67 " pdb=" C4 DG X 67 " model vdw 2.591 2.672 nonbonded pdb=" N1 DG Y 6 " pdb=" C4 DG Y 6 " model vdw 2.591 2.672 ... (remaining 119725 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.300 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.012 0.044 14878 Z= 0.789 Angle : 1.911 8.228 21604 Z= 1.147 Chirality : 0.200 0.637 2424 Planarity : 0.054 0.394 1524 Dihedral : 30.013 175.337 6418 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 0.21 (0.27), residues: 828 helix: 0.63 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.003 ARG A 15 TYR 0.047 0.023 TYR B 44 PHE 0.064 0.034 PHE H 5 TRP 0.065 0.029 TRP B 37 HIS 0.005 0.003 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.79 (14878) covalent geometry : angle 1.91093 / 1.15 (21604) hydrogen bonds : bond 0.28067 / 18.90 ( 731) hydrogen bonds : angle 9.69340 / 7.01 ( 1960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.349 Fit side-chains REVERT: A 11 GLU cc_start: 0.8596 (tt0) cc_final: 0.8322 (tt0) REVERT: A 12 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8324 (ttmm) REVERT: A 28 ASP cc_start: 0.8852 (m-30) cc_final: 0.8625 (m-30) REVERT: A 32 GLU cc_start: 0.8416 (tt0) cc_final: 0.8205 (tt0) REVERT: A 43 LYS cc_start: 0.8759 (mttt) cc_final: 0.8557 (mtpt) REVERT: A 52 SER cc_start: 0.8776 (t) cc_final: 0.8560 (m) REVERT: A 55 LYS cc_start: 0.8875 (mttt) cc_final: 0.8651 (mttp) REVERT: A 58 LYS cc_start: 0.8264 (mttt) cc_final: 0.8029 (mtmt) REVERT: A 60 ASN cc_start: 0.8454 (m-40) cc_final: 0.7662 (OUTLIER) REVERT: B 11 GLU cc_start: 0.8543 (tt0) cc_final: 0.8338 (tt0) REVERT: B 43 LYS cc_start: 0.8689 (mttt) cc_final: 0.8436 (mtpt) REVERT: B 47 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 58 LYS cc_start: 0.8379 (mttt) cc_final: 0.8113 (mtmt) REVERT: B 60 ASN cc_start: 0.8451 (m-40) cc_final: 0.7755 (p0) REVERT: C 12 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8355 (ttpt) REVERT: C 28 ASP cc_start: 0.8769 (m-30) cc_final: 0.8453 (m-30) REVERT: C 58 LYS cc_start: 0.8305 (mttt) cc_final: 0.8081 (mtmt) REVERT: C 60 ASN cc_start: 0.8250 (m-40) cc_final: 0.7706 (p0) REVERT: D 47 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7934 (mm-30) REVERT: D 58 LYS cc_start: 0.8485 (mttt) cc_final: 0.8202 (mtpt) REVERT: D 60 ASN cc_start: 0.8131 (m-40) cc_final: 0.7522 (p0) REVERT: E 39 LYS cc_start: 0.8751 (mttt) cc_final: 0.8529 (mtpt) REVERT: E 43 LYS cc_start: 0.8654 (mttt) cc_final: 0.8390 (mtpt) REVERT: E 58 LYS cc_start: 0.8226 (mttt) cc_final: 0.7987 (mtmt) REVERT: E 60 ASN cc_start: 0.8360 (m-40) cc_final: 0.7553 (OUTLIER) REVERT: F 43 LYS cc_start: 0.8689 (mttt) cc_final: 0.8418 (mtpt) REVERT: F 60 ASN cc_start: 0.8314 (m-40) cc_final: 0.7757 (OUTLIER) REVERT: G 43 LYS cc_start: 0.8634 (mttt) cc_final: 0.8418 (mtpt) REVERT: G 52 SER cc_start: 0.8830 (t) cc_final: 0.8599 (m) REVERT: G 58 LYS cc_start: 0.8293 (mttt) cc_final: 0.8068 (mtmt) REVERT: G 60 ASN cc_start: 0.8223 (m-40) cc_final: 0.7593 (p0) REVERT: H 11 GLU cc_start: 0.8457 (tt0) cc_final: 0.8249 (tt0) REVERT: H 29 LYS cc_start: 0.9033 (tppt) cc_final: 0.8832 (tptt) REVERT: H 39 LYS cc_start: 0.8774 (mttt) cc_final: 0.8459 (mtpt) REVERT: H 55 LYS cc_start: 0.8866 (mttt) cc_final: 0.8665 (mttp) REVERT: H 58 LYS cc_start: 0.8159 (mttt) cc_final: 0.7776 (mtpt) REVERT: H 60 ASN cc_start: 0.8105 (m-40) cc_final: 0.7577 (p0) REVERT: I 12 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8379 (ttpm) REVERT: I 55 LYS cc_start: 0.8850 (mttt) cc_final: 0.8618 (mttp) REVERT: I 60 ASN cc_start: 0.8154 (m-40) cc_final: 0.7329 (p0) REVERT: J 12 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8373 (ttpt) REVERT: J 25 ASP cc_start: 0.8581 (m-30) cc_final: 0.8271 (m-30) REVERT: J 29 LYS cc_start: 0.8819 (tppt) cc_final: 0.8464 (tptt) REVERT: J 32 GLU cc_start: 0.8264 (tt0) cc_final: 0.7764 (mt-10) REVERT: J 43 LYS cc_start: 0.8746 (mttt) cc_final: 0.8523 (mtmp) REVERT: J 60 ASN cc_start: 0.8298 (m-40) cc_final: 0.7726 (OUTLIER) REVERT: K 12 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8491 (ttpt) REVERT: K 43 LYS cc_start: 0.8662 (mttt) cc_final: 0.8437 (mtpt) REVERT: K 60 ASN cc_start: 0.8206 (m-40) cc_final: 0.7479 (p0) REVERT: L 12 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8416 (ttpt) REVERT: L 39 LYS cc_start: 0.8827 (mttt) cc_final: 0.8604 (mtmp) REVERT: L 47 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7956 (mm-30) REVERT: L 58 LYS cc_start: 0.8232 (mttt) cc_final: 0.8028 (mtmm) REVERT: L 60 ASN cc_start: 0.8298 (m-40) cc_final: 0.7706 (OUTLIER) outliers start: 0 outliers final: 5 residues processed: 308 average time/residue: 0.8656 time to fit residues: 283.2536 Evaluate side-chains 263 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN B 51 HIS B 67 GLN C 20 GLN D 51 HIS D 67 GLN E 20 GLN F 51 HIS F 67 GLN G 51 HIS G 67 GLN H 20 GLN H 67 GLN I 16 GLN I 51 HIS I 67 GLN K 16 GLN K 51 HIS K 67 GLN L 67 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125002 restraints weight = 14028.612| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.38 r_work: 0.3194 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14878 Z= 0.192 Angle : 0.838 9.538 21604 Z= 0.465 Chirality : 0.051 0.301 2424 Planarity : 0.007 0.075 1524 Dihedral : 32.671 169.552 4822 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.39 % Allowed : 10.65 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.28), residues: 828 helix: 1.84 (0.19), residues: 648 sheet: None (None), residues: 0 loop : -0.34 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 15 TYR 0.003 0.002 TYR F 44 PHE 0.011 0.003 PHE I 5 TRP 0.029 0.007 TRP L 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.19 (14878) covalent geometry : angle 0.83765 / 0.47 (21604) hydrogen bonds : bond 0.07963 / 5.40 ( 731) hydrogen bonds : angle 3.26380 / 2.34 ( 1960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 264 time to evaluate : 0.349 Fit side-chains REVERT: A 28 ASP cc_start: 0.8666 (m-30) cc_final: 0.8385 (m-30) REVERT: A 43 LYS cc_start: 0.8608 (mttt) cc_final: 0.8366 (mttp) REVERT: A 52 SER cc_start: 0.8637 (t) cc_final: 0.8406 (m) REVERT: A 60 ASN cc_start: 0.8422 (m-40) cc_final: 0.7734 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8302 (m-40) cc_final: 0.7772 (p0) REVERT: C 12 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8337 (ttpt) REVERT: C 28 ASP cc_start: 0.8638 (m-30) cc_final: 0.8328 (m-30) REVERT: C 60 ASN cc_start: 0.8289 (m-40) cc_final: 0.7792 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8160 (m-40) cc_final: 0.7678 (p0) REVERT: E 12 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8480 (tttp) REVERT: E 39 LYS cc_start: 0.8806 (mttt) cc_final: 0.8476 (mtpt) REVERT: E 60 ASN cc_start: 0.8400 (m-40) cc_final: 0.7668 (p0) REVERT: F 1 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5964 (ttm) REVERT: F 60 ASN cc_start: 0.8208 (m-40) cc_final: 0.7749 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8249 (m-40) cc_final: 0.7697 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8775 (mttt) cc_final: 0.8500 (mtpt) REVERT: H 60 ASN cc_start: 0.8143 (m-40) cc_final: 0.7754 (OUTLIER) REVERT: I 60 ASN cc_start: 0.8246 (m-40) cc_final: 0.7512 (p0) REVERT: J 12 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8376 (ttpt) REVERT: J 25 ASP cc_start: 0.8534 (m-30) cc_final: 0.8241 (m-30) REVERT: J 32 GLU cc_start: 0.8288 (tt0) cc_final: 0.7946 (tt0) REVERT: J 60 ASN cc_start: 0.8265 (m-40) cc_final: 0.7771 (OUTLIER) REVERT: K 52 SER cc_start: 0.8623 (t) cc_final: 0.8410 (m) REVERT: K 60 ASN cc_start: 0.8199 (m-40) cc_final: 0.7493 (p0) REVERT: L 39 LYS cc_start: 0.8760 (mttt) cc_final: 0.8473 (mtpt) REVERT: L 60 ASN cc_start: 0.8215 (m-40) cc_final: 0.7761 (OUTLIER) outliers start: 9 outliers final: 10 residues processed: 265 average time/residue: 0.8169 time to fit residues: 230.1709 Evaluate side-chains 250 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 246 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain F residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 109 optimal weight: 40.0000 chunk 103 optimal weight: 40.0000 chunk 119 optimal weight: 40.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 HIS H 20 GLN H 51 HIS L 20 GLN L 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.195214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120304 restraints weight = 13981.428| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.37 r_work: 0.3114 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14878 Z= 0.212 Angle : 0.698 6.466 21604 Z= 0.404 Chirality : 0.045 0.240 2424 Planarity : 0.005 0.054 1524 Dihedral : 32.698 175.043 4822 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.93 % Allowed : 13.43 % Favored : 83.64 % 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: 2.65 (0.27), residues: 828 helix: 2.35 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.49 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 15 TYR 0.006 0.002 TYR K 44 PHE 0.017 0.005 PHE K 5 TRP 0.012 0.003 TRP I 37 HIS 0.004 0.002 HIS G 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (14878) covalent geometry : angle 0.69772 / 0.40 (21604) hydrogen bonds : bond 0.07153 / 4.87 ( 731) hydrogen bonds : angle 3.00826 / 2.14 ( 1960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.308 Fit side-chains REVERT: A 28 ASP cc_start: 0.8683 (m-30) cc_final: 0.8403 (m-30) REVERT: A 43 LYS cc_start: 0.8646 (mttt) cc_final: 0.8396 (mttp) REVERT: A 52 SER cc_start: 0.8631 (t) cc_final: 0.8430 (m) REVERT: A 60 ASN cc_start: 0.8433 (m-40) cc_final: 0.7717 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8852 (ttpp) cc_final: 0.8643 (ttpp) REVERT: B 60 ASN cc_start: 0.8280 (m-40) cc_final: 0.7673 (OUTLIER) REVERT: C 60 ASN cc_start: 0.8348 (m-40) cc_final: 0.7789 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8123 (m-40) cc_final: 0.7655 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8493 (tttp) REVERT: E 39 LYS cc_start: 0.8786 (mttt) cc_final: 0.8498 (mtpt) REVERT: E 60 ASN cc_start: 0.8457 (m-40) cc_final: 0.7674 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8305 (m-40) cc_final: 0.7774 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8291 (m-40) cc_final: 0.7709 (p0) REVERT: H 39 LYS cc_start: 0.8827 (mttt) cc_final: 0.8536 (mtpt) REVERT: H 60 ASN cc_start: 0.8182 (m-40) cc_final: 0.7749 (p0) REVERT: I 12 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8552 (ttpt) REVERT: I 55 LYS cc_start: 0.9076 (mttp) cc_final: 0.8830 (mttp) REVERT: I 60 ASN cc_start: 0.8265 (m-40) cc_final: 0.7435 (OUTLIER) REVERT: J 25 ASP cc_start: 0.8538 (m-30) cc_final: 0.8256 (m-30) REVERT: J 60 ASN cc_start: 0.8282 (m-40) cc_final: 0.7712 (OUTLIER) REVERT: K 52 SER cc_start: 0.8706 (t) cc_final: 0.8414 (m) REVERT: K 60 ASN cc_start: 0.8235 (m-40) cc_final: 0.7507 (p0) REVERT: L 20 GLN cc_start: 0.8790 (tt0) cc_final: 0.8569 (tt0) REVERT: L 39 LYS cc_start: 0.8832 (mttt) cc_final: 0.8559 (mtpt) REVERT: L 60 ASN cc_start: 0.8233 (m-40) cc_final: 0.7754 (OUTLIER) outliers start: 19 outliers final: 16 residues processed: 259 average time/residue: 0.7887 time to fit residues: 218.1784 Evaluate side-chains 253 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 246 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 20 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 116 optimal weight: 40.0000 chunk 86 optimal weight: 40.0000 chunk 50 optimal weight: 0.9980 chunk 106 optimal weight: 40.0000 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 20 GLN I 20 GLN K 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122254 restraints weight = 14055.398| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.37 r_work: 0.3153 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14878 Z= 0.152 Angle : 0.625 7.253 21604 Z= 0.368 Chirality : 0.042 0.218 2424 Planarity : 0.003 0.021 1524 Dihedral : 32.397 173.208 4822 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 16.82 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.27), residues: 828 helix: 2.78 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.35 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 15 TYR 0.010 0.002 TYR E 44 PHE 0.008 0.002 PHE I 5 TRP 0.013 0.003 TRP I 37 HIS 0.002 0.001 HIS D 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (14878) covalent geometry : angle 0.62506 / 0.37 (21604) hydrogen bonds : bond 0.05706 / 3.89 ( 731) hydrogen bonds : angle 2.83675 / 2.02 ( 1960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 0.222 Fit side-chains REVERT: A 28 ASP cc_start: 0.8665 (m-30) cc_final: 0.8357 (m-30) REVERT: A 43 LYS cc_start: 0.8567 (mttt) cc_final: 0.8332 (mttp) REVERT: A 52 SER cc_start: 0.8594 (t) cc_final: 0.8348 (m) REVERT: A 60 ASN cc_start: 0.8412 (m-40) cc_final: 0.7730 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8576 (ttpp) REVERT: B 60 ASN cc_start: 0.8256 (m-40) cc_final: 0.7680 (OUTLIER) REVERT: C 12 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8373 (ttpt) REVERT: C 60 ASN cc_start: 0.8320 (m-40) cc_final: 0.7791 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8052 (m-40) cc_final: 0.7619 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8493 (tttp) REVERT: E 39 LYS cc_start: 0.8817 (mttt) cc_final: 0.8495 (mtpt) REVERT: E 60 ASN cc_start: 0.8396 (m-40) cc_final: 0.7638 (p0) REVERT: F 60 ASN cc_start: 0.8231 (m-40) cc_final: 0.7752 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8232 (m-40) cc_final: 0.7694 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8783 (mttt) cc_final: 0.8474 (mtpt) REVERT: H 60 ASN cc_start: 0.8138 (m-40) cc_final: 0.7738 (p0) REVERT: I 60 ASN cc_start: 0.8259 (m-40) cc_final: 0.7485 (OUTLIER) REVERT: J 25 ASP cc_start: 0.8528 (m-30) cc_final: 0.8237 (m-30) REVERT: J 60 ASN cc_start: 0.8242 (m-40) cc_final: 0.7706 (OUTLIER) REVERT: K 52 SER cc_start: 0.8583 (t) cc_final: 0.8257 (m) REVERT: K 60 ASN cc_start: 0.8241 (m-40) cc_final: 0.7529 (p0) REVERT: L 12 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8336 (tttm) REVERT: L 39 LYS cc_start: 0.8787 (mttt) cc_final: 0.8471 (mtpt) REVERT: L 60 ASN cc_start: 0.8213 (m-40) cc_final: 0.7783 (OUTLIER) outliers start: 15 outliers final: 16 residues processed: 256 average time/residue: 0.8298 time to fit residues: 226.4266 Evaluate side-chains 251 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 244 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain K residue 20 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 40.0000 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 chunk 98 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN C 20 GLN D 4 ASN E 51 HIS F 20 GLN J 51 HIS J 67 GLN L 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.192757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117255 restraints weight = 14181.515| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.40 r_work: 0.3071 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14878 Z= 0.317 Angle : 0.708 6.694 21604 Z= 0.398 Chirality : 0.046 0.244 2424 Planarity : 0.006 0.051 1524 Dihedral : 32.606 170.431 4822 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.24 % Allowed : 16.82 % Favored : 79.94 % 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: 2.63 (0.27), residues: 828 helix: 2.38 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.70 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 50 TYR 0.007 0.002 TYR K 44 PHE 0.012 0.004 PHE L 5 TRP 0.005 0.002 TRP B 37 HIS 0.007 0.003 HIS G 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.32 (14878) covalent geometry : angle 0.70759 / 0.40 (21604) hydrogen bonds : bond 0.08065 / 5.48 ( 731) hydrogen bonds : angle 3.09024 / 2.19 ( 1960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.375 Fit side-chains REVERT: A 28 ASP cc_start: 0.8755 (m-30) cc_final: 0.8502 (m-30) REVERT: A 60 ASN cc_start: 0.8452 (m-40) cc_final: 0.7715 (p0) REVERT: B 60 ASN cc_start: 0.8369 (m-40) cc_final: 0.7739 (p0) REVERT: C 60 ASN cc_start: 0.8339 (m-40) cc_final: 0.7785 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8126 (m-40) cc_final: 0.7627 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8497 (tttp) REVERT: E 60 ASN cc_start: 0.8475 (m-40) cc_final: 0.7704 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8313 (m-40) cc_final: 0.7781 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8369 (m-40) cc_final: 0.7788 (p0) REVERT: H 12 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8477 (tttm) REVERT: H 39 LYS cc_start: 0.8854 (mttt) cc_final: 0.8546 (mtpt) REVERT: H 60 ASN cc_start: 0.8198 (m-40) cc_final: 0.7745 (p0) REVERT: I 60 ASN cc_start: 0.8274 (m-40) cc_final: 0.7468 (p0) REVERT: J 25 ASP cc_start: 0.8589 (m-30) cc_final: 0.8289 (m-30) REVERT: J 60 ASN cc_start: 0.8282 (m-40) cc_final: 0.7651 (p0) REVERT: K 52 SER cc_start: 0.8743 (t) cc_final: 0.8483 (m) REVERT: K 60 ASN cc_start: 0.8302 (m-40) cc_final: 0.7535 (p0) REVERT: L 39 LYS cc_start: 0.8881 (mttt) cc_final: 0.8600 (mtmm) REVERT: L 60 ASN cc_start: 0.8265 (m-40) cc_final: 0.7801 (OUTLIER) outliers start: 21 outliers final: 12 residues processed: 246 average time/residue: 0.8075 time to fit residues: 212.0307 Evaluate side-chains 240 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 233 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 20 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 chunk 118 optimal weight: 50.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 GLN F 20 GLN G 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.194423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119536 restraints weight = 14066.986| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.40 r_work: 0.3096 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14878 Z= 0.181 Angle : 0.659 6.642 21604 Z= 0.377 Chirality : 0.043 0.229 2424 Planarity : 0.004 0.036 1524 Dihedral : 32.565 170.733 4822 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.31 % Allowed : 17.90 % Favored : 79.78 % 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: 2.70 (0.27), residues: 828 helix: 2.43 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.66 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 54 TYR 0.010 0.003 TYR K 44 PHE 0.008 0.002 PHE L 5 TRP 0.007 0.002 TRP E 37 HIS 0.005 0.002 HIS J 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (14878) covalent geometry : angle 0.65940 / 0.38 (21604) hydrogen bonds : bond 0.06710 / 4.57 ( 731) hydrogen bonds : angle 3.09829 / 2.20 ( 1960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.458 Fit side-chains REVERT: A 28 ASP cc_start: 0.8721 (m-30) cc_final: 0.8468 (m-30) REVERT: A 60 ASN cc_start: 0.8419 (m-40) cc_final: 0.7747 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8298 (m-40) cc_final: 0.7736 (p0) REVERT: C 60 ASN cc_start: 0.8311 (m-40) cc_final: 0.7792 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8054 (m-40) cc_final: 0.7599 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8482 (tttp) REVERT: E 60 ASN cc_start: 0.8440 (m-40) cc_final: 0.7702 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8257 (m-40) cc_final: 0.7772 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8336 (m-40) cc_final: 0.7778 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8824 (mttt) cc_final: 0.8511 (mtpt) REVERT: H 60 ASN cc_start: 0.8163 (m-40) cc_final: 0.7753 (p0) REVERT: I 60 ASN cc_start: 0.8286 (m-40) cc_final: 0.7495 (p0) REVERT: J 25 ASP cc_start: 0.8544 (m-30) cc_final: 0.8248 (m-30) REVERT: J 60 ASN cc_start: 0.8281 (m-40) cc_final: 0.7714 (p0) REVERT: K 52 SER cc_start: 0.8692 (t) cc_final: 0.8442 (m) REVERT: K 60 ASN cc_start: 0.8292 (m-40) cc_final: 0.7565 (p0) REVERT: L 39 LYS cc_start: 0.8868 (mttt) cc_final: 0.8575 (mtpt) REVERT: L 60 ASN cc_start: 0.8227 (m-40) cc_final: 0.7803 (OUTLIER) outliers start: 15 outliers final: 17 residues processed: 243 average time/residue: 0.8026 time to fit residues: 208.3522 Evaluate side-chains 248 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 238 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 106 optimal weight: 40.0000 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 117 optimal weight: 40.0000 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.194283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119273 restraints weight = 14059.234| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.40 r_work: 0.3096 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14878 Z= 0.207 Angle : 0.655 6.636 21604 Z= 0.374 Chirality : 0.043 0.231 2424 Planarity : 0.003 0.030 1524 Dihedral : 32.520 170.253 4822 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.16 % Allowed : 18.36 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.27), residues: 828 helix: 2.52 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.61 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 50 TYR 0.010 0.002 TYR K 44 PHE 0.007 0.002 PHE H 5 TRP 0.008 0.002 TRP E 37 HIS 0.004 0.002 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (14878) covalent geometry : angle 0.65524 / 0.37 (21604) hydrogen bonds : bond 0.06825 / 4.64 ( 731) hydrogen bonds : angle 3.01928 / 2.14 ( 1960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.315 Fit side-chains REVERT: A 28 ASP cc_start: 0.8728 (m-30) cc_final: 0.8453 (m-30) REVERT: A 60 ASN cc_start: 0.8431 (m-40) cc_final: 0.7750 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8329 (m-40) cc_final: 0.7746 (p0) REVERT: C 60 ASN cc_start: 0.8333 (m-40) cc_final: 0.7802 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8081 (m-40) cc_final: 0.7615 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8505 (tttp) REVERT: E 60 ASN cc_start: 0.8462 (m-40) cc_final: 0.7718 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8273 (m-40) cc_final: 0.7775 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8345 (m-40) cc_final: 0.7778 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8841 (mttt) cc_final: 0.8513 (mtpt) REVERT: H 60 ASN cc_start: 0.8174 (m-40) cc_final: 0.7770 (p0) REVERT: I 60 ASN cc_start: 0.8296 (m-40) cc_final: 0.7499 (p0) REVERT: J 25 ASP cc_start: 0.8543 (m-30) cc_final: 0.8244 (m-30) REVERT: J 60 ASN cc_start: 0.8292 (m-40) cc_final: 0.7700 (p0) REVERT: K 52 SER cc_start: 0.8699 (t) cc_final: 0.8442 (m) REVERT: K 60 ASN cc_start: 0.8300 (m-40) cc_final: 0.7562 (p0) REVERT: L 39 LYS cc_start: 0.8886 (mttt) cc_final: 0.8588 (mtpt) REVERT: L 60 ASN cc_start: 0.8245 (m-40) cc_final: 0.7815 (OUTLIER) outliers start: 14 outliers final: 18 residues processed: 241 average time/residue: 0.7108 time to fit residues: 182.8532 Evaluate side-chains 246 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.195308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119996 restraints weight = 14044.611| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.42 r_work: 0.3105 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14878 Z= 0.155 Angle : 0.635 7.570 21604 Z= 0.367 Chirality : 0.042 0.224 2424 Planarity : 0.003 0.025 1524 Dihedral : 32.481 170.646 4822 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.85 % Allowed : 18.36 % Favored : 79.78 % 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: 2.97 (0.27), residues: 828 helix: 2.61 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.55 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 15 TYR 0.011 0.003 TYR F 44 PHE 0.007 0.002 PHE A 5 TRP 0.007 0.002 TRP E 37 HIS 0.003 0.001 HIS K 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (14878) covalent geometry : angle 0.63472 / 0.37 (21604) hydrogen bonds : bond 0.06274 / 4.27 ( 731) hydrogen bonds : angle 3.02645 / 2.14 ( 1960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.364 Fit side-chains REVERT: A 28 ASP cc_start: 0.8721 (m-30) cc_final: 0.8467 (m-30) REVERT: A 60 ASN cc_start: 0.8412 (m-40) cc_final: 0.7752 (OUTLIER) REVERT: B 12 LYS cc_start: 0.8864 (ttpp) cc_final: 0.8641 (ttpp) REVERT: B 60 ASN cc_start: 0.8288 (m-40) cc_final: 0.7725 (p0) REVERT: C 60 ASN cc_start: 0.8311 (m-40) cc_final: 0.7790 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8071 (m-40) cc_final: 0.7611 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8484 (tttp) REVERT: E 60 ASN cc_start: 0.8444 (m-40) cc_final: 0.7712 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8251 (m-40) cc_final: 0.7777 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8326 (m-40) cc_final: 0.7770 (OUTLIER) REVERT: H 39 LYS cc_start: 0.8814 (mttt) cc_final: 0.8493 (mtpt) REVERT: H 60 ASN cc_start: 0.8172 (m-40) cc_final: 0.7779 (p0) REVERT: I 60 ASN cc_start: 0.8283 (m-40) cc_final: 0.7503 (p0) REVERT: J 25 ASP cc_start: 0.8529 (m-30) cc_final: 0.8226 (m-30) REVERT: J 60 ASN cc_start: 0.8279 (m-40) cc_final: 0.7720 (p0) REVERT: K 52 SER cc_start: 0.8635 (t) cc_final: 0.8403 (m) REVERT: K 60 ASN cc_start: 0.8275 (m-40) cc_final: 0.7546 (p0) REVERT: L 39 LYS cc_start: 0.8871 (mttt) cc_final: 0.8575 (mtpt) REVERT: L 60 ASN cc_start: 0.8227 (m-40) cc_final: 0.7810 (OUTLIER) outliers start: 12 outliers final: 15 residues processed: 244 average time/residue: 0.7320 time to fit residues: 190.6800 Evaluate side-chains 249 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 30.0000 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 30.0000 chunk 91 optimal weight: 40.0000 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 40.0000 chunk 4 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.195281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120195 restraints weight = 14217.230| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.40 r_work: 0.3115 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14878 Z= 0.185 Angle : 0.624 6.663 21604 Z= 0.363 Chirality : 0.041 0.223 2424 Planarity : 0.003 0.020 1524 Dihedral : 32.385 170.451 4822 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.54 % Allowed : 18.67 % Favored : 79.78 % 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: 3.06 (0.27), residues: 828 helix: 2.67 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 54 TYR 0.012 0.003 TYR I 44 PHE 0.008 0.002 PHE H 5 TRP 0.009 0.002 TRP E 37 HIS 0.003 0.001 HIS J 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (14878) covalent geometry : angle 0.62374 / 0.36 (21604) hydrogen bonds : bond 0.06394 / 4.34 ( 731) hydrogen bonds : angle 2.93146 / 2.08 ( 1960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 242 time to evaluate : 0.369 Fit side-chains REVERT: A 28 ASP cc_start: 0.8741 (m-30) cc_final: 0.8473 (m-30) REVERT: A 60 ASN cc_start: 0.8432 (m-40) cc_final: 0.7779 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8319 (m-40) cc_final: 0.7770 (p0) REVERT: C 60 ASN cc_start: 0.8349 (m-40) cc_final: 0.7838 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8065 (m-40) cc_final: 0.7635 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8536 (tttp) REVERT: E 60 ASN cc_start: 0.8444 (m-40) cc_final: 0.7735 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8288 (m-40) cc_final: 0.7819 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8336 (m-40) cc_final: 0.7799 (OUTLIER) REVERT: H 12 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8495 (tttm) REVERT: H 39 LYS cc_start: 0.8832 (mttt) cc_final: 0.8522 (mtpt) REVERT: H 60 ASN cc_start: 0.8180 (m-40) cc_final: 0.7799 (p0) REVERT: I 60 ASN cc_start: 0.8296 (m-40) cc_final: 0.7545 (p0) REVERT: J 25 ASP cc_start: 0.8541 (m-30) cc_final: 0.8247 (m-30) REVERT: J 60 ASN cc_start: 0.8266 (m-40) cc_final: 0.7739 (p0) REVERT: K 52 SER cc_start: 0.8682 (t) cc_final: 0.8434 (m) REVERT: K 60 ASN cc_start: 0.8301 (m-40) cc_final: 0.7590 (p0) REVERT: L 39 LYS cc_start: 0.8884 (mttt) cc_final: 0.8595 (mtpt) REVERT: L 60 ASN cc_start: 0.8244 (m-40) cc_final: 0.7840 (OUTLIER) outliers start: 10 outliers final: 16 residues processed: 245 average time/residue: 0.8457 time to fit residues: 220.9752 Evaluate side-chains 247 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 92 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 20 GLN K 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.195545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121510 restraints weight = 14167.232| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.37 r_work: 0.3137 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14878 Z= 0.179 Angle : 0.599 6.536 21604 Z= 0.352 Chirality : 0.040 0.221 2424 Planarity : 0.003 0.024 1524 Dihedral : 32.204 170.821 4822 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.27), residues: 828 helix: 2.78 (0.17), residues: 648 sheet: None (None), residues: 0 loop : -0.46 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 15 TYR 0.012 0.003 TYR I 44 PHE 0.006 0.002 PHE F 5 TRP 0.012 0.003 TRP E 37 HIS 0.003 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (14878) covalent geometry : angle 0.59873 / 0.35 (21604) hydrogen bonds : bond 0.06048 / 4.12 ( 731) hydrogen bonds : angle 2.89329 / 2.06 ( 1960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 242 time to evaluate : 0.356 Fit side-chains REVERT: A 28 ASP cc_start: 0.8724 (m-30) cc_final: 0.8433 (m-30) REVERT: A 60 ASN cc_start: 0.8420 (m-40) cc_final: 0.7774 (OUTLIER) REVERT: B 60 ASN cc_start: 0.8331 (m-40) cc_final: 0.7771 (p0) REVERT: C 60 ASN cc_start: 0.8332 (m-40) cc_final: 0.7820 (OUTLIER) REVERT: D 60 ASN cc_start: 0.8072 (m-40) cc_final: 0.7648 (OUTLIER) REVERT: E 12 LYS cc_start: 0.8818 (ttpp) cc_final: 0.8529 (tttp) REVERT: E 60 ASN cc_start: 0.8454 (m-40) cc_final: 0.7754 (OUTLIER) REVERT: F 60 ASN cc_start: 0.8275 (m-40) cc_final: 0.7794 (OUTLIER) REVERT: G 60 ASN cc_start: 0.8294 (m-40) cc_final: 0.7762 (OUTLIER) REVERT: H 12 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8484 (tttm) REVERT: H 39 LYS cc_start: 0.8811 (mttt) cc_final: 0.8491 (mtpt) REVERT: H 60 ASN cc_start: 0.8141 (m-40) cc_final: 0.7756 (OUTLIER) REVERT: I 60 ASN cc_start: 0.8303 (m-40) cc_final: 0.7546 (p0) REVERT: J 25 ASP cc_start: 0.8501 (m-30) cc_final: 0.8209 (m-30) REVERT: J 60 ASN cc_start: 0.8241 (m-40) cc_final: 0.7705 (p0) REVERT: K 28 ASP cc_start: 0.8400 (m-30) cc_final: 0.8196 (m-30) REVERT: K 52 SER cc_start: 0.8648 (t) cc_final: 0.8365 (m) REVERT: K 60 ASN cc_start: 0.8275 (m-40) cc_final: 0.7570 (p0) REVERT: L 39 LYS cc_start: 0.8874 (mttt) cc_final: 0.8585 (mtpt) REVERT: L 60 ASN cc_start: 0.8239 (m-40) cc_final: 0.7831 (OUTLIER) outliers start: 8 outliers final: 14 residues processed: 245 average time/residue: 0.7245 time to fit residues: 189.4895 Evaluate side-chains 246 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 240 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain K residue 41 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 40.0000 chunk 29 optimal weight: 0.6980 chunk 102 optimal weight: 30.0000 chunk 47 optimal weight: 0.6980 chunk 113 optimal weight: 40.0000 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 4 ASN K 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.196593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123162 restraints weight = 14179.521| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.35 r_work: 0.3158 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14878 Z= 0.137 Angle : 0.583 6.466 21604 Z= 0.346 Chirality : 0.039 0.215 2424 Planarity : 0.002 0.017 1524 Dihedral : 32.170 171.225 4822 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.93 % Allowed : 20.37 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.27), residues: 828 helix: 2.98 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.45 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 15 TYR 0.012 0.003 TYR I 44 PHE 0.006 0.002 PHE H 5 TRP 0.013 0.002 TRP E 37 HIS 0.002 0.001 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (14878) covalent geometry : angle 0.58305 / 0.35 (21604) hydrogen bonds : bond 0.05522 / 3.76 ( 731) hydrogen bonds : angle 2.89591 / 2.05 ( 1960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5103.65 seconds wall clock time: 87 minutes 22.12 seconds (5242.12 seconds total)