Starting phenix.real_space_refine on Fri Sep 11 21:50:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg6_31106/09_2026/7eg6_31106.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg6_31106/09_2026/7eg6_31106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eg6_31106/09_2026/7eg6_31106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg6_31106/09_2026/7eg6_31106.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eg6_31106/09_2026/7eg6_31106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg6_31106/09_2026/7eg6_31106.map" } resolution = 3.1 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= 0.001 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 292 5.49 5 S 12 5.16 5 C 6692 2.51 5 N 2277 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12118 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 159 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 2.63, per 1000 atoms: 0.22 Number of scatterers: 12118 At special positions: 0 Unit cell: (83.7876, 120.31, 129.978, 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 12 16.00 P 292 15.00 O 2845 8.00 N 2277 7.00 C 6692 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: 0.98 Conformation dependent library (CDL) restraints added in 353.4 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.0% alpha, 2.8% beta 144 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'M' and resid 665 through 680 removed outlier: 3.794A pdb=" N ASP M 670 " --> pdb=" O ASP M 666 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR M 671 " --> pdb=" O LYS M 667 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG M 676 " --> pdb=" O ARG M 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.585A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.544A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.503A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.655A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.555A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.640A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.561A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.514A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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 removed outlier: 3.878A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.603A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.443A 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 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.552A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.841A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.880A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.307A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.972A 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: 7.119A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 78 410 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.35 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: 2035 1.33 - 1.45: 4332 1.45 - 1.56: 5953 1.56 - 1.68: 582 1.68 - 1.80: 22 Bond restraints: 12924 Sorted by residual: bond pdb=" C1' DG I 3 " pdb=" N9 DG I 3 " ideal model delta sigma weight residual 1.468 1.383 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" C1' DT I 145 " pdb=" N1 DT I 145 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.01e+01 bond pdb=" C1' DA I 147 " pdb=" N9 DA I 147 " ideal model delta sigma weight residual 1.468 1.393 0.075 1.40e-02 5.10e+03 2.87e+01 bond pdb=" C1' DT J 1 " pdb=" N1 DT J 1 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.83e+01 bond pdb=" C1' DC J 145 " pdb=" N1 DC J 145 " ideal model delta sigma weight residual 1.468 1.538 -0.070 1.40e-02 5.10e+03 2.46e+01 ... (remaining 12919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17266 1.66 - 3.33: 1389 3.33 - 4.99: 46 4.99 - 6.65: 11 6.65 - 8.32: 3 Bond angle restraints: 18715 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.20 4.90 9.70e-01 1.06e+00 2.55e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 119.70 125.64 -5.94 1.20e+00 6.94e-01 2.45e+01 angle pdb=" O5' DA I 131 " pdb=" C5' DA I 131 " pdb=" C4' DA I 131 " ideal model delta sigma weight residual 109.40 113.15 -3.75 8.00e-01 1.56e+00 2.20e+01 angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 ... (remaining 18710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.95: 5346 29.95 - 59.89: 1618 59.89 - 89.84: 49 89.84 - 119.78: 0 119.78 - 149.73: 3 Dihedral angle restraints: 7016 sinusoidal: 4758 harmonic: 2258 Sorted by residual: dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 70.27 149.73 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 79.88 140.12 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 -18.31 -121.69 1 3.50e+01 8.16e-04 1.20e+01 ... (remaining 7013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1408 0.046 - 0.093: 565 0.093 - 0.139: 141 0.139 - 0.185: 21 0.185 - 0.232: 2 Chirality restraints: 2137 Sorted by residual: chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" P DG J 95 " pdb=" OP1 DG J 95 " pdb=" OP2 DG J 95 " pdb=" O5' DG J 95 " both_signs ideal model delta sigma weight residual True 2.34 -2.55 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C4' DA I 131 " pdb=" C5' DA I 131 " pdb=" O4' DA I 131 " pdb=" C3' DA I 131 " both_signs ideal model delta sigma weight residual False -2.53 -2.37 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2134 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.77e+00 pdb=" N PRO G 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO E 121 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO C 80 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3622 2.86 - 3.37: 9941 3.37 - 3.88: 24177 3.88 - 4.39: 27558 4.39 - 4.90: 38877 Nonbonded interactions: 104175 Sorted by model distance: nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.348 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.357 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.374 3.040 nonbonded pdb=" O LEU E 92 " pdb=" OG SER E 96 " model vdw 2.374 3.040 ... (remaining 104170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 : 0.008 0.085 12924 Z= 0.676 Angle : 0.882 8.319 18715 Z= 0.746 Chirality : 0.052 0.232 2137 Planarity : 0.006 0.060 1362 Dihedral : 27.432 149.731 5558 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.24), residues: 761 helix: -0.88 (0.17), residues: 551 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 49 TYR 0.011 0.002 TYR C 50 PHE 0.012 0.002 PHE B 61 HIS 0.009 0.002 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.68 (12924) covalent geometry : angle 0.88160 / 0.75 (18715) hydrogen bonds : bond 0.14096 / 9.33 ( 780) hydrogen bonds : angle 4.55852 / 3.24 ( 1955) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8621 (m-40) cc_final: 0.8087 (m-40) REVERT: B 59 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8676 (ttmm) REVERT: C 92 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8168 (mt-10) REVERT: D 73 GLU cc_start: 0.8984 (tp30) cc_final: 0.8693 (tp30) REVERT: D 80 TYR cc_start: 0.8016 (m-10) cc_final: 0.7648 (m-10) REVERT: D 90 GLU cc_start: 0.8538 (mp0) cc_final: 0.7198 (mp0) REVERT: E 90 MET cc_start: 0.8641 (mmm) cc_final: 0.8440 (mmp) REVERT: F 31 LYS cc_start: 0.9081 (tttt) cc_final: 0.8831 (tttp) REVERT: F 88 TYR cc_start: 0.9078 (m-10) cc_final: 0.8818 (m-80) REVERT: G 73 ASN cc_start: 0.8943 (m110) cc_final: 0.8638 (t0) REVERT: H 39 TYR cc_start: 0.8196 (t80) cc_final: 0.7758 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1615 time to fit residues: 37.9985 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 55 GLN A 68 GLN A 76 GLN B 93 GLN C 104 GLN D 79 HIS D 92 GLN E 68 GLN E 125 GLN F 25 ASN F 93 GLN G 73 ASN G 110 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055055 restraints weight = 33437.130| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.15 r_work: 0.2629 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12924 Z= 0.165 Angle : 0.660 6.999 18715 Z= 0.383 Chirality : 0.046 0.276 2137 Planarity : 0.005 0.047 1362 Dihedral : 30.938 153.642 4058 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.94 % Allowed : 7.86 % Favored : 91.19 % 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: 1.04 (0.28), residues: 761 helix: 1.38 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -1.25 (0.34), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.010 0.001 TYR C 57 PHE 0.007 0.001 PHE B 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (12924) covalent geometry : angle 0.66002 / 0.38 (18715) hydrogen bonds : bond 0.04943 / 3.39 ( 780) hydrogen bonds : angle 2.93964 / 2.12 ( 1955) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8387 (mtp85) cc_final: 0.8081 (mmt90) REVERT: B 59 LYS cc_start: 0.9224 (ttpt) cc_final: 0.8867 (ttmm) REVERT: C 74 LYS cc_start: 0.9082 (mptt) cc_final: 0.8858 (mmmt) REVERT: D 39 TYR cc_start: 0.8801 (t80) cc_final: 0.8247 (t80) REVERT: D 68 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8436 (mm-30) REVERT: D 73 GLU cc_start: 0.9269 (tp30) cc_final: 0.8918 (tp30) REVERT: D 90 GLU cc_start: 0.8971 (mp0) cc_final: 0.8611 (mp0) REVERT: E 90 MET cc_start: 0.9097 (mmm) cc_final: 0.8892 (mmp) REVERT: F 25 ASN cc_start: 0.8793 (m110) cc_final: 0.8164 (m-40) REVERT: F 84 MET cc_start: 0.8972 (mmm) cc_final: 0.8503 (mmm) REVERT: F 88 TYR cc_start: 0.9329 (m-10) cc_final: 0.9073 (m-80) REVERT: G 62 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9372 (tt) REVERT: G 73 ASN cc_start: 0.8920 (m-40) cc_final: 0.8594 (t0) REVERT: H 39 TYR cc_start: 0.8597 (t80) cc_final: 0.8262 (t80) REVERT: H 76 ARG cc_start: 0.8991 (ttm-80) cc_final: 0.8693 (ttm110) outliers start: 6 outliers final: 1 residues processed: 167 average time/residue: 0.1459 time to fit residues: 32.7344 Evaluate side-chains 161 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 159 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 94 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN C 38 ASN C 104 GLN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.053886 restraints weight = 34003.583| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.14 r_work: 0.2596 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12924 Z= 0.229 Angle : 0.668 7.083 18715 Z= 0.377 Chirality : 0.046 0.289 2137 Planarity : 0.004 0.040 1362 Dihedral : 31.221 153.617 4058 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.63 % Allowed : 8.96 % Favored : 90.41 % 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: 2.09 (0.30), residues: 761 helix: 2.26 (0.22), residues: 563 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.012 0.001 TYR A 54 PHE 0.009 0.002 PHE D 62 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (12924) covalent geometry : angle 0.66819 / 0.38 (18715) hydrogen bonds : bond 0.05342 / 3.65 ( 780) hydrogen bonds : angle 2.84662 / 2.04 ( 1955) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 153 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8275 (mmt90) REVERT: A 105 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 25 ASN cc_start: 0.8799 (m-40) cc_final: 0.8065 (m-40) REVERT: B 59 LYS cc_start: 0.9250 (ttpt) cc_final: 0.8915 (ttmm) REVERT: D 68 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8488 (mm-30) REVERT: D 73 GLU cc_start: 0.9292 (tp30) cc_final: 0.8965 (tp30) REVERT: D 90 GLU cc_start: 0.9004 (mp0) cc_final: 0.8761 (mp0) REVERT: F 84 MET cc_start: 0.9078 (mmm) cc_final: 0.8696 (mmm) REVERT: F 88 TYR cc_start: 0.9332 (m-10) cc_final: 0.9110 (m-80) REVERT: G 62 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9374 (tt) REVERT: G 73 ASN cc_start: 0.8990 (m-40) cc_final: 0.8621 (t0) REVERT: H 39 TYR cc_start: 0.8711 (t80) cc_final: 0.8371 (t80) REVERT: H 76 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8858 (ttm110) outliers start: 4 outliers final: 1 residues processed: 153 average time/residue: 0.1474 time to fit residues: 29.9307 Evaluate side-chains 149 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.082162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.054630 restraints weight = 33734.982| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.13 r_work: 0.2619 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12924 Z= 0.167 Angle : 0.619 7.052 18715 Z= 0.356 Chirality : 0.044 0.293 2137 Planarity : 0.004 0.039 1362 Dihedral : 31.164 153.403 4058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 10.22 % Favored : 89.15 % 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: 2.50 (0.30), residues: 761 helix: 2.53 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -1.08 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.012 0.001 TYR H 118 PHE 0.011 0.001 PHE B 61 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (12924) covalent geometry : angle 0.61911 / 0.36 (18715) hydrogen bonds : bond 0.04357 / 3.00 ( 780) hydrogen bonds : angle 2.70566 / 1.93 ( 1955) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8270 (mmt90) REVERT: A 64 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8629 (mmtp) REVERT: A 105 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 25 ASN cc_start: 0.8708 (m-40) cc_final: 0.7950 (m-40) REVERT: D 68 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8500 (mm-30) REVERT: D 73 GLU cc_start: 0.9300 (tp30) cc_final: 0.8953 (tp30) REVERT: D 80 TYR cc_start: 0.7982 (m-10) cc_final: 0.7747 (m-80) REVERT: D 90 GLU cc_start: 0.8997 (mp0) cc_final: 0.8773 (mp0) REVERT: E 90 MET cc_start: 0.8912 (mmp) cc_final: 0.8650 (mmp) REVERT: F 84 MET cc_start: 0.9045 (mmm) cc_final: 0.8588 (mmm) REVERT: F 88 TYR cc_start: 0.9364 (m-10) cc_final: 0.9103 (m-80) REVERT: G 73 ASN cc_start: 0.8991 (m-40) cc_final: 0.8621 (t0) REVERT: H 39 TYR cc_start: 0.8530 (t80) cc_final: 0.8125 (t80) REVERT: H 76 ARG cc_start: 0.9090 (ttm-80) cc_final: 0.8852 (ttm110) outliers start: 4 outliers final: 1 residues processed: 164 average time/residue: 0.1480 time to fit residues: 32.3246 Evaluate side-chains 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.054431 restraints weight = 33984.359| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.14 r_work: 0.2611 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12924 Z= 0.186 Angle : 0.631 7.351 18715 Z= 0.358 Chirality : 0.044 0.292 2137 Planarity : 0.004 0.040 1362 Dihedral : 31.188 153.419 4058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.63 % Allowed : 11.64 % Favored : 87.74 % 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: 2.64 (0.30), residues: 761 helix: 2.63 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -1.03 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 67 TYR 0.013 0.001 TYR H 118 PHE 0.011 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (12924) covalent geometry : angle 0.63112 / 0.36 (18715) hydrogen bonds : bond 0.04558 / 3.13 ( 780) hydrogen bonds : angle 2.69845 / 1.92 ( 1955) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8257 (mmt90) REVERT: A 64 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8652 (mmtp) REVERT: A 105 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8620 (mt-10) REVERT: B 25 ASN cc_start: 0.8644 (m-40) cc_final: 0.7721 (m110) REVERT: D 68 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8494 (mm-30) REVERT: D 73 GLU cc_start: 0.9296 (tp30) cc_final: 0.8969 (tp30) REVERT: D 80 TYR cc_start: 0.7917 (m-10) cc_final: 0.7695 (m-80) REVERT: E 90 MET cc_start: 0.8949 (mmp) cc_final: 0.8677 (mmp) REVERT: G 73 ASN cc_start: 0.9018 (m-40) cc_final: 0.8635 (t0) REVERT: H 39 TYR cc_start: 0.8488 (t80) cc_final: 0.8061 (t80) REVERT: H 76 ARG cc_start: 0.9112 (ttm-80) cc_final: 0.8905 (ttm110) outliers start: 4 outliers final: 2 residues processed: 159 average time/residue: 0.1439 time to fit residues: 30.7895 Evaluate side-chains 154 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.0000 chunk 85 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054903 restraints weight = 33785.757| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.12 r_work: 0.2629 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12924 Z= 0.146 Angle : 0.604 7.081 18715 Z= 0.348 Chirality : 0.043 0.293 2137 Planarity : 0.004 0.035 1362 Dihedral : 31.128 153.091 4058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 11.95 % Favored : 87.58 % 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: 2.76 (0.30), residues: 761 helix: 2.71 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 67 TYR 0.014 0.001 TYR F 88 PHE 0.010 0.001 PHE B 61 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (12924) covalent geometry : angle 0.60434 / 0.35 (18715) hydrogen bonds : bond 0.04175 / 2.87 ( 780) hydrogen bonds : angle 2.60894 / 1.86 ( 1955) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8249 (mtt-85) REVERT: A 105 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8625 (mt-10) REVERT: B 25 ASN cc_start: 0.8637 (m-40) cc_final: 0.7697 (m110) REVERT: C 64 GLU cc_start: 0.8427 (tp30) cc_final: 0.8168 (tp30) REVERT: D 39 TYR cc_start: 0.8717 (t80) cc_final: 0.8253 (t80) REVERT: D 68 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8466 (mm-30) REVERT: D 73 GLU cc_start: 0.9291 (tp30) cc_final: 0.8953 (tp30) REVERT: E 90 MET cc_start: 0.8941 (mmp) cc_final: 0.8696 (mmp) REVERT: F 84 MET cc_start: 0.9109 (mmm) cc_final: 0.8515 (mmm) REVERT: F 88 TYR cc_start: 0.9301 (m-80) cc_final: 0.8920 (m-80) REVERT: G 73 ASN cc_start: 0.9003 (m-40) cc_final: 0.8643 (t0) REVERT: H 39 TYR cc_start: 0.8430 (t80) cc_final: 0.8026 (t80) REVERT: H 76 ARG cc_start: 0.9034 (ttm-80) cc_final: 0.8788 (ttm170) outliers start: 3 outliers final: 2 residues processed: 161 average time/residue: 0.1260 time to fit residues: 27.7844 Evaluate side-chains 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.055678 restraints weight = 33861.203| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.17 r_work: 0.2649 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12924 Z= 0.133 Angle : 0.591 8.838 18715 Z= 0.343 Chirality : 0.042 0.288 2137 Planarity : 0.004 0.043 1362 Dihedral : 31.011 152.739 4058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 11.95 % Favored : 87.58 % 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 (0.30), residues: 761 helix: 2.75 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 67 TYR 0.012 0.001 TYR H 118 PHE 0.010 0.001 PHE B 61 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (12924) covalent geometry : angle 0.59071 / 0.34 (18715) hydrogen bonds : bond 0.03943 / 2.72 ( 780) hydrogen bonds : angle 2.53862 / 1.80 ( 1955) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8161 (mtt-85) REVERT: A 64 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8623 (mmtp) REVERT: B 25 ASN cc_start: 0.8553 (m-40) cc_final: 0.7596 (m110) REVERT: C 74 LYS cc_start: 0.9206 (mmmt) cc_final: 0.9001 (mptt) REVERT: D 39 TYR cc_start: 0.8745 (t80) cc_final: 0.8252 (t80) REVERT: D 68 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8467 (mm-30) REVERT: D 73 GLU cc_start: 0.9296 (tp30) cc_final: 0.8963 (tp30) REVERT: D 90 GLU cc_start: 0.8896 (mp0) cc_final: 0.8080 (mp0) REVERT: E 90 MET cc_start: 0.8911 (mmp) cc_final: 0.8652 (mmp) REVERT: F 84 MET cc_start: 0.9083 (mmm) cc_final: 0.8765 (mmm) REVERT: F 88 TYR cc_start: 0.9283 (m-80) cc_final: 0.8947 (m-80) REVERT: G 73 ASN cc_start: 0.8993 (m-40) cc_final: 0.8660 (t0) REVERT: H 39 TYR cc_start: 0.8384 (t80) cc_final: 0.7942 (t80) outliers start: 3 outliers final: 1 residues processed: 160 average time/residue: 0.1436 time to fit residues: 31.0237 Evaluate side-chains 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 104 GLN E 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055169 restraints weight = 33764.856| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.13 r_work: 0.2636 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12924 Z= 0.166 Angle : 0.607 7.119 18715 Z= 0.349 Chirality : 0.043 0.284 2137 Planarity : 0.004 0.040 1362 Dihedral : 31.074 152.551 4058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.47 % Allowed : 13.05 % Favored : 86.48 % 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: 2.88 (0.30), residues: 761 helix: 2.78 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.013 0.001 TYR H 118 PHE 0.010 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (12924) covalent geometry : angle 0.60726 / 0.35 (18715) hydrogen bonds : bond 0.04244 / 2.91 ( 780) hydrogen bonds : angle 2.59838 / 1.84 ( 1955) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8544 (mtp85) cc_final: 0.8243 (mtt-85) REVERT: A 64 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8628 (mmtp) REVERT: B 25 ASN cc_start: 0.8562 (m-40) cc_final: 0.7596 (m110) REVERT: D 39 TYR cc_start: 0.8784 (t80) cc_final: 0.8279 (t80) REVERT: D 68 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8493 (mm-30) REVERT: D 73 GLU cc_start: 0.9289 (tp30) cc_final: 0.8958 (tp30) REVERT: E 90 MET cc_start: 0.8950 (mmp) cc_final: 0.8717 (mmp) REVERT: F 84 MET cc_start: 0.9097 (mmm) cc_final: 0.8763 (mmm) REVERT: F 88 TYR cc_start: 0.9293 (m-10) cc_final: 0.8928 (m-80) REVERT: G 73 ASN cc_start: 0.8994 (m-40) cc_final: 0.8668 (t0) REVERT: H 39 TYR cc_start: 0.8423 (t80) cc_final: 0.7966 (t80) outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 0.1474 time to fit residues: 30.5574 Evaluate side-chains 154 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.082294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054583 restraints weight = 33633.718| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.15 r_work: 0.2615 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12924 Z= 0.201 Angle : 0.638 7.641 18715 Z= 0.360 Chirality : 0.044 0.289 2137 Planarity : 0.004 0.042 1362 Dihedral : 31.207 152.303 4058 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.31 % Allowed : 12.74 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.30), residues: 761 helix: 2.74 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.87 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 67 TYR 0.017 0.002 TYR D 80 PHE 0.010 0.002 PHE B 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (12924) covalent geometry : angle 0.63804 / 0.36 (18715) hydrogen bonds : bond 0.04493 / 3.08 ( 780) hydrogen bonds : angle 2.69013 / 1.91 ( 1955) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8275 (mtt-85) REVERT: A 64 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8661 (mmtp) REVERT: A 105 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8639 (mt-10) REVERT: B 25 ASN cc_start: 0.8620 (m-40) cc_final: 0.7632 (m110) REVERT: D 39 TYR cc_start: 0.8805 (t80) cc_final: 0.8301 (t80) REVERT: D 68 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8505 (mm-30) REVERT: D 73 GLU cc_start: 0.9301 (tp30) cc_final: 0.8986 (tp30) REVERT: D 90 GLU cc_start: 0.8919 (mp0) cc_final: 0.8038 (mp0) REVERT: E 90 MET cc_start: 0.8956 (mmp) cc_final: 0.8730 (mmp) REVERT: F 84 MET cc_start: 0.9141 (mmm) cc_final: 0.8844 (mmm) REVERT: F 88 TYR cc_start: 0.9266 (m-10) cc_final: 0.8955 (m-80) REVERT: G 73 ASN cc_start: 0.9036 (m-40) cc_final: 0.8694 (t0) REVERT: H 39 TYR cc_start: 0.8479 (t80) cc_final: 0.8046 (t80) outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.1448 time to fit residues: 29.8319 Evaluate side-chains 153 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.054803 restraints weight = 33742.465| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.16 r_work: 0.2628 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12924 Z= 0.159 Angle : 0.621 7.614 18715 Z= 0.353 Chirality : 0.043 0.291 2137 Planarity : 0.004 0.038 1362 Dihedral : 31.183 152.229 4058 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.31 % Allowed : 12.74 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.30), residues: 761 helix: 2.75 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.016 0.002 TYR D 80 PHE 0.010 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (12924) covalent geometry : angle 0.62082 / 0.35 (18715) hydrogen bonds : bond 0.04256 / 2.93 ( 780) hydrogen bonds : angle 2.65213 / 1.88 ( 1955) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8550 (mtp85) cc_final: 0.8226 (mtt-85) REVERT: A 64 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8653 (mmtp) REVERT: A 105 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8627 (mt-10) REVERT: B 25 ASN cc_start: 0.8609 (m-40) cc_final: 0.7598 (m110) REVERT: D 39 TYR cc_start: 0.8831 (t80) cc_final: 0.8296 (t80) REVERT: D 68 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8500 (mm-30) REVERT: D 73 GLU cc_start: 0.9296 (tp30) cc_final: 0.8973 (tp30) REVERT: D 90 GLU cc_start: 0.8901 (mp0) cc_final: 0.8024 (mp0) REVERT: E 90 MET cc_start: 0.8945 (mmp) cc_final: 0.8709 (mmp) REVERT: F 84 MET cc_start: 0.9120 (mmm) cc_final: 0.8823 (mmm) REVERT: F 88 TYR cc_start: 0.9262 (m-10) cc_final: 0.8953 (m-80) REVERT: G 73 ASN cc_start: 0.9026 (m-40) cc_final: 0.8694 (t0) REVERT: H 39 TYR cc_start: 0.8432 (t80) cc_final: 0.7992 (t80) outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.1369 time to fit residues: 29.0369 Evaluate side-chains 155 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055127 restraints weight = 33696.247| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.15 r_work: 0.2635 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12924 Z= 0.146 Angle : 0.610 7.362 18715 Z= 0.350 Chirality : 0.043 0.291 2137 Planarity : 0.004 0.037 1362 Dihedral : 31.144 152.149 4058 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.31 % Allowed : 12.42 % Favored : 87.26 % 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: 761 helix: 2.78 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 67 TYR 0.017 0.001 TYR B 88 PHE 0.010 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (12924) covalent geometry : angle 0.61003 / 0.35 (18715) hydrogen bonds : bond 0.04117 / 2.83 ( 780) hydrogen bonds : angle 2.62756 / 1.86 ( 1955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2990.37 seconds wall clock time: 51 minutes 49.60 seconds (3109.60 seconds total)