Starting phenix.real_space_refine on Wed Aug 5 18:57:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlb_36391/08_2026/8jlb_36391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlb_36391/08_2026/8jlb_36391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2026/8jlb_36391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2026/8jlb_36391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2026/8jlb_36391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2026/8jlb_36391.map" } resolution = 2.36 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= 0.005 sd= 0.050 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 289 5.49 5 S 10 5.16 5 C 6540 2.51 5 N 2221 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 11844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.14, per 1000 atoms: 0.18 Number of scatterers: 11844 At special positions: 0 Unit cell: (117.66, 110.24, 116.6, 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 10 16.00 P 289 15.00 O 2784 8.00 N 2221 7.00 C 6540 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: 0.64 Conformation dependent library (CDL) restraints added in 158.8 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.0% alpha, 3.2% beta 144 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.981A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.421A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.998A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.504A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.901A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.166A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.485A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.979A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.294A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2141 1.33 - 1.45: 4215 1.45 - 1.57: 5692 1.57 - 1.69: 577 1.69 - 1.81: 20 Bond restraints: 12645 Sorted by residual: bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.55e+01 bond pdb=" C3' DG I -53 " pdb=" C2' DG I -53 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DC I -62 " pdb=" C2' DC I -62 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.21e+01 bond pdb=" C3' DG J -22 " pdb=" C2' DG J -22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 ... (remaining 12640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17088 1.81 - 3.61: 1172 3.61 - 5.42: 57 5.42 - 7.22: 3 7.22 - 9.03: 1 Bond angle restraints: 18321 Sorted by residual: angle pdb=" O5' DA I -45 " pdb=" C5' DA I -45 " pdb=" C4' DA I -45 " ideal model delta sigma weight residual 109.40 114.04 -4.64 8.00e-01 1.56e+00 3.37e+01 angle pdb=" O4' DA I -45 " pdb=" C4' DA I -45 " pdb=" C3' DA I -45 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.23e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 111.93 -3.93 7.00e-01 2.04e+00 3.16e+01 angle pdb=" O5' DA I 50 " pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 109.40 113.88 -4.48 8.00e-01 1.56e+00 3.13e+01 angle pdb=" O4' DT J -16 " pdb=" C1' DT J -16 " pdb=" N1 DT J -16 " ideal model delta sigma weight residual 108.00 111.32 -3.32 7.00e-01 2.04e+00 2.25e+01 ... (remaining 18316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 4319 21.34 - 42.68: 1358 42.68 - 64.02: 1117 64.02 - 85.37: 51 85.37 - 106.71: 4 Dihedral angle restraints: 6849 sinusoidal: 4697 harmonic: 2152 Sorted by residual: dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 55.63 -55.63 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CG ARG E 131 " pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.86 44.86 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.79 44.79 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1200 0.034 - 0.068: 634 0.068 - 0.102: 212 0.102 - 0.136: 34 0.136 - 0.171: 3 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA ARG A 129 " pdb=" N ARG A 129 " pdb=" C ARG A 129 " pdb=" CB ARG A 129 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 2080 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " 0.903 9.50e-02 1.11e+02 4.05e-01 9.94e+01 pdb=" NE ARG A 129 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " -0.028 2.00e-02 2.50e+03 1.66e-02 6.19e+00 pdb=" N1 DC I 69 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.030 2.00e-02 2.50e+03 1.35e-02 5.46e+00 pdb=" N9 DG I 47 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 20 2.57 - 3.15: 8418 3.15 - 3.74: 21350 3.74 - 4.32: 30563 4.32 - 4.90: 43287 Nonbonded interactions: 103638 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 1.988 3.040 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.133 2.496 nonbonded pdb=" OG SER C 40 " pdb=" O SER D 87 " model vdw 2.215 3.040 nonbonded pdb=" OG SER H 36 " pdb=" ND2 ASN H 63 " model vdw 2.305 3.120 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.382 3.120 ... (remaining 103633 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 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: 0.320 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.360 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 0.034 12645 Z= 0.531 Angle : 0.858 9.028 18321 Z= 0.759 Chirality : 0.044 0.171 2083 Planarity : 0.012 0.405 1316 Dihedral : 29.909 106.706 5465 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.16 % Allowed : 18.34 % Favored : 81.49 % 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: 0.69 (0.28), residues: 730 helix: 0.83 (0.20), residues: 534 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 42 TYR 0.019 0.002 TYR F 88 PHE 0.008 0.001 PHE A 84 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.53 (12645) covalent geometry : angle 0.85772 / 0.76 (18321) hydrogen bonds : bond 0.07193 / 4.79 ( 781) hydrogen bonds : angle 3.38801 / 2.56 ( 1948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: C 84 GLN cc_start: 0.8654 (tp40) cc_final: 0.8440 (tp40) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 1.0624 time to fit residues: 123.5561 Evaluate side-chains 102 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108186 restraints weight = 15750.451| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.71 r_work: 0.3394 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12645 Z= 0.147 Angle : 0.665 6.804 18321 Z= 0.389 Chirality : 0.050 0.232 2083 Planarity : 0.004 0.036 1316 Dihedral : 31.697 104.298 4005 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.97 % Allowed : 17.53 % Favored : 81.49 % 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: 3.00 (0.30), residues: 730 helix: 2.74 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.23 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.012 0.001 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (12645) covalent geometry : angle 0.66479 / 0.39 (18321) hydrogen bonds : bond 0.05548 / 3.77 ( 781) hydrogen bonds : angle 2.99294 / 2.26 ( 1948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.303 Fit side-chains REVERT: E 58 THR cc_start: 0.8612 (p) cc_final: 0.8217 (t) REVERT: E 133 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6836 (mp0) outliers start: 6 outliers final: 2 residues processed: 119 average time/residue: 1.0268 time to fit residues: 128.1404 Evaluate side-chains 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 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 = 0.3632 r_free = 0.3632 target = 0.118058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106960 restraints weight = 15853.392| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.73 r_work: 0.3385 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12645 Z= 0.151 Angle : 0.634 8.356 18321 Z= 0.372 Chirality : 0.047 0.215 2083 Planarity : 0.004 0.040 1316 Dihedral : 31.224 110.313 4003 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.14 % Allowed : 16.88 % Favored : 81.98 % 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: 3.37 (0.31), residues: 730 helix: 3.02 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.09 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 129 TYR 0.014 0.002 TYR D 121 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12645) covalent geometry : angle 0.63351 / 0.37 (18321) hydrogen bonds : bond 0.05147 / 3.50 ( 781) hydrogen bonds : angle 2.81722 / 2.14 ( 1948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.305 Fit side-chains REVERT: E 58 THR cc_start: 0.8645 (p) cc_final: 0.8231 (t) REVERT: E 133 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: G 114 VAL cc_start: 0.8783 (p) cc_final: 0.8472 (t) outliers start: 7 outliers final: 4 residues processed: 123 average time/residue: 0.9929 time to fit residues: 128.3846 Evaluate side-chains 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100200 restraints weight = 15808.139| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 0.73 r_work: 0.3283 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 12645 Z= 0.308 Angle : 0.796 7.735 18321 Z= 0.441 Chirality : 0.060 0.306 2083 Planarity : 0.006 0.048 1316 Dihedral : 30.990 111.469 4003 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.95 % Allowed : 16.72 % Favored : 81.33 % 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: 2.47 (0.30), residues: 730 helix: 2.34 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 17 TYR 0.023 0.003 TYR D 121 PHE 0.012 0.002 PHE D 70 HIS 0.006 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.31 (12645) covalent geometry : angle 0.79600 / 0.44 (18321) hydrogen bonds : bond 0.07173 / 4.86 ( 781) hydrogen bonds : angle 3.12485 / 2.36 ( 1948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 91 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.4605 (tt0) REVERT: E 58 THR cc_start: 0.8711 (p) cc_final: 0.8310 (t) REVERT: E 133 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: F 93 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7999 (mm-40) REVERT: G 91 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6228 (tp30) outliers start: 12 outliers final: 3 residues processed: 117 average time/residue: 1.0970 time to fit residues: 134.2372 Evaluate side-chains 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 10.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101963 restraints weight = 15765.128| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.73 r_work: 0.3311 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12645 Z= 0.171 Angle : 0.725 10.018 18321 Z= 0.409 Chirality : 0.053 0.247 2083 Planarity : 0.005 0.043 1316 Dihedral : 31.008 112.802 4003 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.95 % Allowed : 17.37 % Favored : 80.68 % 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: 2.68 (0.30), residues: 730 helix: 2.49 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 129 TYR 0.017 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (12645) covalent geometry : angle 0.72466 / 0.41 (18321) hydrogen bonds : bond 0.06192 / 4.18 ( 781) hydrogen bonds : angle 3.02485 / 2.28 ( 1948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 57 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7951 (t) REVERT: A 65 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 91 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.4392 (tt0) REVERT: E 58 THR cc_start: 0.8693 (p) cc_final: 0.8293 (t) REVERT: E 131 ARG cc_start: 0.8464 (mtt180) cc_final: 0.8183 (mtt180) REVERT: E 133 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6803 (mp0) outliers start: 12 outliers final: 2 residues processed: 126 average time/residue: 1.0771 time to fit residues: 141.9649 Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102385 restraints weight = 15801.234| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.73 r_work: 0.3318 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12645 Z= 0.156 Angle : 0.703 7.213 18321 Z= 0.400 Chirality : 0.052 0.250 2083 Planarity : 0.004 0.039 1316 Dihedral : 31.005 113.582 4003 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.30 % Allowed : 17.69 % Favored : 81.01 % 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: 2.81 (0.30), residues: 730 helix: 2.61 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.34 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.016 0.002 TYR D 121 PHE 0.007 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (12645) covalent geometry : angle 0.70292 / 0.40 (18321) hydrogen bonds : bond 0.05985 / 4.05 ( 781) hydrogen bonds : angle 2.97327 / 2.25 ( 1948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8390 (tp) REVERT: C 91 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.4383 (tt0) REVERT: E 58 THR cc_start: 0.8689 (p) cc_final: 0.8299 (t) REVERT: E 133 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: G 91 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.3886 (tp30) outliers start: 8 outliers final: 4 residues processed: 123 average time/residue: 1.0720 time to fit residues: 138.0578 Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102670 restraints weight = 15773.069| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.73 r_work: 0.3323 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12645 Z= 0.165 Angle : 0.693 7.042 18321 Z= 0.395 Chirality : 0.052 0.250 2083 Planarity : 0.004 0.040 1316 Dihedral : 31.013 114.461 4003 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.62 % Allowed : 18.02 % Favored : 80.36 % 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: 2.86 (0.30), residues: 730 helix: 2.66 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 77 TYR 0.015 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (12645) covalent geometry : angle 0.69325 / 0.39 (18321) hydrogen bonds : bond 0.05906 / 4.01 ( 781) hydrogen bonds : angle 2.95068 / 2.23 ( 1948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8380 (tp) REVERT: C 91 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.4085 (tp30) REVERT: E 58 THR cc_start: 0.8688 (p) cc_final: 0.8297 (t) REVERT: E 133 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: G 91 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.3893 (tp30) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 1.0300 time to fit residues: 133.9776 Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.114480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103680 restraints weight = 15866.827| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 0.72 r_work: 0.3326 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12645 Z= 0.179 Angle : 0.673 6.798 18321 Z= 0.385 Chirality : 0.050 0.237 2083 Planarity : 0.004 0.040 1316 Dihedral : 30.952 118.928 4003 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.79 % Allowed : 17.86 % Favored : 80.36 % 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: 2.91 (0.30), residues: 730 helix: 2.69 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.015 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (12645) covalent geometry : angle 0.67310 / 0.39 (18321) hydrogen bonds : bond 0.05743 / 3.91 ( 781) hydrogen bonds : angle 2.88217 / 2.18 ( 1948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8373 (tp) REVERT: C 91 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.4448 (tt0) REVERT: D 62 MET cc_start: 0.9004 (mmm) cc_final: 0.8796 (mmt) REVERT: E 58 THR cc_start: 0.8706 (p) cc_final: 0.8310 (t) REVERT: E 133 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6906 (mp0) outliers start: 11 outliers final: 4 residues processed: 125 average time/residue: 1.0108 time to fit residues: 132.5350 Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.114896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104097 restraints weight = 15640.152| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.72 r_work: 0.3332 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12645 Z= 0.144 Angle : 0.663 6.793 18321 Z= 0.383 Chirality : 0.049 0.237 2083 Planarity : 0.004 0.040 1316 Dihedral : 30.955 119.088 4003 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.30 % Allowed : 18.02 % Favored : 80.68 % 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: 3.00 (0.30), residues: 730 helix: 2.76 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 129 TYR 0.014 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (12645) covalent geometry : angle 0.66292 / 0.38 (18321) hydrogen bonds : bond 0.05597 / 3.81 ( 781) hydrogen bonds : angle 2.87618 / 2.17 ( 1948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8361 (tp) REVERT: C 91 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.4434 (tt0) REVERT: D 62 MET cc_start: 0.9003 (mmm) cc_final: 0.8791 (mmt) REVERT: E 58 THR cc_start: 0.8703 (p) cc_final: 0.8306 (t) REVERT: E 133 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6894 (mp0) outliers start: 8 outliers final: 4 residues processed: 125 average time/residue: 1.0290 time to fit residues: 134.8336 Evaluate side-chains 124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.114893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104064 restraints weight = 15845.198| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.72 r_work: 0.3332 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12645 Z= 0.158 Angle : 0.663 6.804 18321 Z= 0.381 Chirality : 0.050 0.236 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.954 119.409 4003 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.30 % Allowed : 18.18 % Favored : 80.52 % 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: 3.01 (0.30), residues: 730 helix: 2.77 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.29 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.014 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12645) covalent geometry : angle 0.66290 / 0.38 (18321) hydrogen bonds : bond 0.05599 / 3.82 ( 781) hydrogen bonds : angle 2.86865 / 2.17 ( 1948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8363 (tp) REVERT: C 91 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.4440 (tt0) REVERT: D 62 MET cc_start: 0.9008 (mmm) cc_final: 0.8793 (mmt) REVERT: E 58 THR cc_start: 0.8706 (p) cc_final: 0.8309 (t) REVERT: E 133 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6905 (mp0) outliers start: 8 outliers final: 4 residues processed: 123 average time/residue: 1.0306 time to fit residues: 133.0733 Evaluate side-chains 125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.114993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104180 restraints weight = 15746.804| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.72 r_work: 0.3334 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12645 Z= 0.146 Angle : 0.659 6.781 18321 Z= 0.380 Chirality : 0.049 0.236 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.954 119.413 4003 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.14 % Allowed : 18.67 % Favored : 80.19 % 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: 3.04 (0.30), residues: 730 helix: 2.79 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.014 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (12645) covalent geometry : angle 0.65920 / 0.38 (18321) hydrogen bonds : bond 0.05566 / 3.79 ( 781) hydrogen bonds : angle 2.86413 / 2.17 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.01 seconds wall clock time: 76 minutes 26.65 seconds (4586.65 seconds total)