Starting phenix.real_space_refine on Fri Jul 3 03:21:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eg6_31106/07_2026/7eg6_31106.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eg6_31106/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7eg6_31106/07_2026/7eg6_31106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eg6_31106/07_2026/7eg6_31106.map" model { file = "/net/cci-nas-00/data/ceres_data/7eg6_31106/07_2026/7eg6_31106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eg6_31106/07_2026/7eg6_31106.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.76, per 1000 atoms: 0.23 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: 1.00 Conformation dependent library (CDL) restraints added in 244.4 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: 1.62 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: 1.32 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: 17290 1.66 - 3.33: 1366 3.33 - 4.99: 45 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=" 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 angle pdb=" O5' DG I 121 " pdb=" C5' DG I 121 " pdb=" C4' DG I 121 " ideal model delta sigma weight residual 109.40 113.07 -3.67 8.00e-01 1.56e+00 2.10e+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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.900 Find NCS groups from input model: 0.130 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- 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= 0.675 Angle : 0.874 8.319 18715 Z= 0.739 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 0.87355 / 0.74 (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 : 0.355 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: 0.8167 (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: 0.7199 (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: 0.8843 (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: 0.8639 (t0) REVERT: H 39 TYR cc_start: 0.8196 (t80) cc_final: 0.7766 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1636 time to fit residues: 38.3897 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 : 0.321 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.3456 r_free = 0.3456 target = 0.082422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.054997 restraints weight = 33428.804| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.13 r_work: 0.2627 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12924 Z= 0.169 Angle : 0.641 6.518 18715 Z= 0.382 Chirality : 0.045 0.257 2137 Planarity : 0.005 0.046 1362 Dihedral : 30.948 154.459 4058 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.79 % Allowed : 8.33 % Favored : 90.88 % 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: 1.01 (0.28), residues: 761 helix: 1.37 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.26 (0.34), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 76 TYR 0.010 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.17 (12924) covalent geometry : angle 0.64064 / 0.38 (18715) hydrogen bonds : bond 0.05067 / 3.47 ( 780) hydrogen bonds : angle 2.97580 / 2.15 ( 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: 5 poor density : 167 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8390 (mtp85) cc_final: 0.8030 (mtt-85) REVERT: B 59 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8861 (ttmm) REVERT: D 39 TYR cc_start: 0.8799 (t80) cc_final: 0.8243 (t80) REVERT: D 68 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8435 (mm-30) REVERT: D 73 GLU cc_start: 0.9278 (tp30) cc_final: 0.8934 (tp30) REVERT: D 80 TYR cc_start: 0.7979 (m-10) cc_final: 0.7662 (m-10) REVERT: D 90 GLU cc_start: 0.8972 (mp0) cc_final: 0.8603 (mp0) REVERT: E 90 MET cc_start: 0.9089 (mmm) cc_final: 0.8885 (mmp) REVERT: F 25 ASN cc_start: 0.8795 (m110) cc_final: 0.8150 (m-40) REVERT: F 84 MET cc_start: 0.9013 (mmm) cc_final: 0.8486 (mmm) REVERT: F 88 TYR cc_start: 0.9319 (m-10) cc_final: 0.9053 (m-80) REVERT: G 62 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9380 (tt) REVERT: G 73 ASN cc_start: 0.8921 (m-40) cc_final: 0.8598 (t0) REVERT: H 39 TYR cc_start: 0.8597 (t80) cc_final: 0.8271 (t80) REVERT: H 76 ARG cc_start: 0.8994 (ttm-80) cc_final: 0.8693 (ttm110) outliers start: 5 outliers final: 1 residues processed: 168 average time/residue: 0.1451 time to fit residues: 32.4357 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 : 0.308 ------------------------------------------------------------------------------- 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: 0.5980 chunk 89 optimal weight: 10.9990 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: 0.6980 chunk 94 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN C 38 ASN C 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.053940 restraints weight = 33884.261| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.16 r_work: 0.2602 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.218 Angle : 0.646 7.004 18715 Z= 0.371 Chirality : 0.045 0.277 2137 Planarity : 0.004 0.041 1362 Dihedral : 31.272 154.762 4058 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 9.12 % 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: 2.25 (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 0.005 0.000 ARG H 30 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 0.00436 / 0.22 (12924) covalent geometry : angle 0.64561 / 0.37 (18715) hydrogen bonds : bond 0.05150 / 3.53 ( 780) hydrogen bonds : angle 2.83079 / 2.03 ( 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 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8189 (mtt-85) REVERT: A 105 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8641 (mt-10) REVERT: B 25 ASN cc_start: 0.8795 (m-40) cc_final: 0.8104 (m-40) REVERT: B 59 LYS cc_start: 0.9239 (ttpt) cc_final: 0.8908 (ttmm) REVERT: D 68 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8480 (mm-30) REVERT: D 73 GLU cc_start: 0.9286 (tp30) cc_final: 0.8967 (tp30) REVERT: D 90 GLU cc_start: 0.9017 (mp0) cc_final: 0.8786 (mp0) REVERT: F 84 MET cc_start: 0.9068 (mmm) cc_final: 0.8717 (mmm) REVERT: F 88 TYR cc_start: 0.9333 (m-10) cc_final: 0.9116 (m-80) REVERT: G 62 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9367 (tt) REVERT: G 73 ASN cc_start: 0.8978 (m-40) cc_final: 0.8621 (t0) REVERT: H 39 TYR cc_start: 0.8697 (t80) cc_final: 0.8344 (t80) REVERT: H 65 ASP cc_start: 0.9358 (t70) cc_final: 0.9117 (t0) REVERT: H 76 ARG cc_start: 0.9090 (ttm-80) cc_final: 0.8841 (ttm110) outliers start: 3 outliers final: 1 residues processed: 153 average time/residue: 0.1509 time to fit residues: 30.5409 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 : 0.320 ------------------------------------------------------------------------------- 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: 0.0970 chunk 78 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN 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 = 0.3464 r_free = 0.3464 target = 0.082696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055233 restraints weight = 33732.489| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.14 r_work: 0.2636 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12924 Z= 0.143 Angle : 0.585 6.435 18715 Z= 0.346 Chirality : 0.042 0.277 2137 Planarity : 0.004 0.038 1362 Dihedral : 31.161 154.625 4058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.47 % Allowed : 10.69 % Favored : 88.84 % 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: 2.51 (0.30), residues: 761 helix: 2.52 (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 0.012 0.001 TYR H 118 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (12924) covalent geometry : angle 0.58508 / 0.35 (18715) hydrogen bonds : bond 0.04179 / 2.88 ( 780) hydrogen bonds : angle 2.64355 / 1.89 ( 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 168 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8173 (mtt-85) REVERT: B 25 ASN cc_start: 0.8648 (m-40) cc_final: 0.7942 (m-40) REVERT: D 56 MET cc_start: 0.9563 (tpt) cc_final: 0.9298 (tpt) REVERT: D 68 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8483 (mm-30) REVERT: D 73 GLU cc_start: 0.9245 (tp30) cc_final: 0.8862 (tp30) REVERT: D 90 GLU cc_start: 0.8993 (mp0) cc_final: 0.8787 (mp0) REVERT: D 96 ARG cc_start: 0.9232 (mtm-85) cc_final: 0.8888 (mtp180) REVERT: F 84 MET cc_start: 0.9016 (mmm) cc_final: 0.8596 (mmm) REVERT: F 88 TYR cc_start: 0.9332 (m-10) cc_final: 0.9065 (m-80) REVERT: G 62 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9326 (tt) REVERT: G 73 ASN cc_start: 0.8968 (m-40) cc_final: 0.8628 (t0) REVERT: H 39 TYR cc_start: 0.8466 (t80) cc_final: 0.8045 (t80) REVERT: H 65 ASP cc_start: 0.9329 (t70) cc_final: 0.9083 (t0) REVERT: H 76 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8857 (ttm110) outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.1467 time to fit residues: 32.3899 Evaluate side-chains 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 38 ASN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054464 restraints weight = 34007.687| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.20 r_work: 0.2607 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12924 Z= 0.198 Angle : 0.617 7.165 18715 Z= 0.356 Chirality : 0.044 0.275 2137 Planarity : 0.004 0.036 1362 Dihedral : 31.235 154.745 4058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.47 % Allowed : 11.64 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.30), residues: 761 helix: 2.68 (0.22), residues: 563 sheet: None (None), residues: 0 loop : -0.99 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.016 0.001 TYR D 80 PHE 0.009 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (12924) covalent geometry : angle 0.61723 / 0.36 (18715) hydrogen bonds : bond 0.04592 / 3.15 ( 780) hydrogen bonds : angle 2.70322 / 1.93 ( 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 154 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8140 (mtt-85) REVERT: A 64 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8635 (mmtp) REVERT: A 105 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8639 (mt-10) REVERT: B 24 ASP cc_start: 0.7263 (t0) cc_final: 0.7062 (t0) REVERT: B 25 ASN cc_start: 0.8586 (m-40) cc_final: 0.7704 (m110) REVERT: D 68 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8485 (mm-30) REVERT: D 73 GLU cc_start: 0.9285 (tp30) cc_final: 0.8926 (tp30) REVERT: G 62 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9347 (tt) REVERT: G 73 ASN cc_start: 0.8985 (m-40) cc_final: 0.8635 (t0) REVERT: H 39 TYR cc_start: 0.8506 (t80) cc_final: 0.8095 (t80) REVERT: H 65 ASP cc_start: 0.9349 (t70) cc_final: 0.9096 (t0) REVERT: H 76 ARG cc_start: 0.9131 (ttm-80) cc_final: 0.8929 (ttm110) outliers start: 3 outliers final: 1 residues processed: 153 average time/residue: 0.1428 time to fit residues: 29.1148 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 84 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.082924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055454 restraints weight = 33741.745| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.14 r_work: 0.2639 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12924 Z= 0.139 Angle : 0.581 7.824 18715 Z= 0.342 Chirality : 0.042 0.278 2137 Planarity : 0.004 0.039 1362 Dihedral : 31.158 154.309 4058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 12.26 % 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: 2.78 (0.30), residues: 761 helix: 2.71 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.90 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.022 0.002 TYR D 80 PHE 0.009 0.001 PHE B 61 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (12924) covalent geometry : angle 0.58137 / 0.34 (18715) hydrogen bonds : bond 0.04056 / 2.79 ( 780) hydrogen bonds : angle 2.58381 / 1.84 ( 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 165 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 162 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8548 (mtp85) cc_final: 0.8042 (mtt-85) REVERT: A 64 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8618 (mmtp) REVERT: A 105 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8621 (mt-10) REVERT: B 25 ASN cc_start: 0.8572 (m-40) cc_final: 0.7665 (m110) REVERT: B 88 TYR cc_start: 0.8961 (m-10) cc_final: 0.8673 (m-10) REVERT: C 74 LYS cc_start: 0.9221 (mmmt) cc_final: 0.9013 (mptt) REVERT: D 39 TYR cc_start: 0.8749 (t80) cc_final: 0.8248 (t80) REVERT: D 68 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8473 (mm-30) REVERT: D 73 GLU cc_start: 0.9270 (tp30) cc_final: 0.8897 (tp30) REVERT: F 84 MET cc_start: 0.9047 (mmm) cc_final: 0.8700 (mmm) REVERT: G 62 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9322 (tt) REVERT: G 73 ASN cc_start: 0.8986 (m-40) cc_final: 0.8653 (t0) REVERT: H 39 TYR cc_start: 0.8409 (t80) cc_final: 0.7973 (t80) REVERT: H 65 ASP cc_start: 0.9329 (t70) cc_final: 0.9079 (t0) outliers start: 3 outliers final: 1 residues processed: 163 average time/residue: 0.1389 time to fit residues: 30.1736 Evaluate side-chains 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.082972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055303 restraints weight = 33759.401| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.15 r_work: 0.2641 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12924 Z= 0.147 Angle : 0.581 6.885 18715 Z= 0.342 Chirality : 0.042 0.272 2137 Planarity : 0.004 0.038 1362 Dihedral : 31.118 154.234 4058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 13.36 % Favored : 86.16 % 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: 563 sheet: None (None), residues: 0 loop : -0.81 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.031 0.002 TYR D 80 PHE 0.009 0.001 PHE B 61 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12924) covalent geometry : angle 0.58125 / 0.34 (18715) hydrogen bonds : bond 0.04101 / 2.82 ( 780) hydrogen bonds : angle 2.57858 / 1.83 ( 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 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8097 (mtt-85) REVERT: A 64 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8620 (mmtp) REVERT: B 25 ASN cc_start: 0.8526 (m-40) cc_final: 0.7599 (m110) REVERT: D 39 TYR cc_start: 0.8774 (t80) cc_final: 0.8273 (t80) REVERT: D 68 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8489 (mm-30) REVERT: D 73 GLU cc_start: 0.9281 (tp30) cc_final: 0.8909 (tp30) REVERT: G 62 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9322 (tt) REVERT: G 73 ASN cc_start: 0.8982 (m-40) cc_final: 0.8663 (t0) REVERT: G 92 GLU cc_start: 0.8663 (mt-10) cc_final: 0.6578 (mt-10) REVERT: H 39 TYR cc_start: 0.8406 (t80) cc_final: 0.7976 (t80) REVERT: H 65 ASP cc_start: 0.9331 (t70) cc_final: 0.9082 (t0) outliers start: 3 outliers final: 1 residues processed: 156 average time/residue: 0.1340 time to fit residues: 28.1542 Evaluate side-chains 157 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 62 ILE 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: 0.7980 chunk 92 optimal weight: 7.9990 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: 0.7980 chunk 74 optimal weight: 9.9990 chunk 54 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.055594 restraints weight = 33828.329| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.17 r_work: 0.2643 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12924 Z= 0.146 Angle : 0.580 7.238 18715 Z= 0.341 Chirality : 0.041 0.271 2137 Planarity : 0.004 0.037 1362 Dihedral : 31.103 153.966 4058 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.63 % Allowed : 13.36 % Favored : 86.01 % 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: 2.91 (0.30), residues: 761 helix: 2.79 (0.22), residues: 563 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 67 TYR 0.034 0.002 TYR F 88 PHE 0.009 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (12924) covalent geometry : angle 0.58016 / 0.34 (18715) hydrogen bonds : bond 0.04022 / 2.77 ( 780) hydrogen bonds : angle 2.55322 / 1.80 ( 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 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8138 (mtt-85) REVERT: A 64 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8616 (mmtp) REVERT: B 25 ASN cc_start: 0.8538 (m-40) cc_final: 0.7584 (m110) REVERT: D 39 TYR cc_start: 0.8764 (t80) cc_final: 0.8281 (t80) REVERT: D 68 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8494 (mm-30) REVERT: D 73 GLU cc_start: 0.9283 (tp30) cc_final: 0.8904 (tp30) REVERT: D 90 GLU cc_start: 0.8880 (mp0) cc_final: 0.7993 (mp0) REVERT: G 62 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9312 (tt) REVERT: G 73 ASN cc_start: 0.8976 (m-40) cc_final: 0.8671 (t0) REVERT: G 94 ASN cc_start: 0.9233 (t0) cc_final: 0.9029 (t0) REVERT: H 39 TYR cc_start: 0.8388 (t80) cc_final: 0.7938 (t80) REVERT: H 65 ASP cc_start: 0.9330 (t70) cc_final: 0.9076 (t0) outliers start: 4 outliers final: 1 residues processed: 158 average time/residue: 0.1366 time to fit residues: 28.6891 Evaluate side-chains 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 62 ILE 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: 0.0040 chunk 77 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 0.0980 chunk 90 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.054893 restraints weight = 33622.655| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.16 r_work: 0.2631 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2050 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= 0.179 Angle : 0.604 7.654 18715 Z= 0.350 Chirality : 0.042 0.270 2137 Planarity : 0.004 0.046 1362 Dihedral : 31.197 153.882 4058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 13.36 % Favored : 86.16 % 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: 2.89 (0.30), residues: 761 helix: 2.77 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 67 TYR 0.025 0.002 TYR D 80 PHE 0.009 0.001 PHE B 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (12924) covalent geometry : angle 0.60415 / 0.35 (18715) hydrogen bonds : bond 0.04339 / 2.97 ( 780) hydrogen bonds : angle 2.62534 / 1.85 ( 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 158 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8156 (mtt-85) REVERT: A 64 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8631 (mmtp) REVERT: A 105 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8628 (mt-10) REVERT: B 25 ASN cc_start: 0.8534 (m-40) cc_final: 0.7542 (m110) REVERT: D 39 TYR cc_start: 0.8789 (t80) cc_final: 0.8298 (t80) REVERT: D 68 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8515 (mm-30) REVERT: D 73 GLU cc_start: 0.9296 (tp30) cc_final: 0.8939 (tp30) REVERT: D 90 GLU cc_start: 0.8900 (mp0) cc_final: 0.8012 (mp0) REVERT: F 85 ASP cc_start: 0.9397 (m-30) cc_final: 0.9184 (m-30) REVERT: G 73 ASN cc_start: 0.8987 (m-40) cc_final: 0.8676 (t0) REVERT: H 39 TYR cc_start: 0.8438 (t80) cc_final: 0.7971 (t80) REVERT: H 65 ASP cc_start: 0.9344 (t70) cc_final: 0.9088 (t0) REVERT: H 76 ARG cc_start: 0.9170 (ttm170) cc_final: 0.8851 (mtp85) outliers start: 3 outliers final: 1 residues processed: 156 average time/residue: 0.1454 time to fit residues: 30.3993 Evaluate side-chains 156 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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: 0.1980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 104 GLN E 68 GLN F 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055309 restraints weight = 33820.957| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.17 r_work: 0.2643 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2113 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= 0.146 Angle : 0.587 7.220 18715 Z= 0.343 Chirality : 0.042 0.274 2137 Planarity : 0.004 0.038 1362 Dihedral : 31.177 153.755 4058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.05 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: 2.92 (0.30), residues: 761 helix: 2.78 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 67 TYR 0.041 0.002 TYR B 88 PHE 0.009 0.001 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (12924) covalent geometry : angle 0.58742 / 0.34 (18715) hydrogen bonds : bond 0.04089 / 2.81 ( 780) hydrogen bonds : angle 2.58893 / 1.82 ( 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 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8163 (mtt-85) REVERT: A 64 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8628 (mmtp) REVERT: A 105 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8633 (mt-10) REVERT: B 25 ASN cc_start: 0.8481 (m-40) cc_final: 0.7496 (m110) REVERT: D 39 TYR cc_start: 0.8768 (t80) cc_final: 0.8277 (t80) REVERT: D 68 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8501 (mm-30) REVERT: D 73 GLU cc_start: 0.9287 (tp30) cc_final: 0.8925 (tp30) REVERT: D 90 GLU cc_start: 0.8890 (mp0) cc_final: 0.8026 (mp0) REVERT: F 85 ASP cc_start: 0.9354 (m-30) cc_final: 0.9143 (m-30) REVERT: G 73 ASN cc_start: 0.9042 (m-40) cc_final: 0.8680 (t0) REVERT: H 39 TYR cc_start: 0.8390 (t80) cc_final: 0.7927 (t80) REVERT: H 65 ASP cc_start: 0.9333 (t70) cc_final: 0.9075 (t0) REVERT: H 76 ARG cc_start: 0.9168 (ttm170) cc_final: 0.8877 (mtp85) outliers start: 3 outliers final: 1 residues processed: 158 average time/residue: 0.1432 time to fit residues: 30.3402 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 : 0.308 ------------------------------------------------------------------------------- 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: 0.6980 chunk 77 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.082998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.055473 restraints weight = 33771.966| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.13 r_work: 0.2650 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12924 Z= 0.151 Angle : 0.583 6.981 18715 Z= 0.342 Chirality : 0.042 0.271 2137 Planarity : 0.004 0.044 1362 Dihedral : 31.132 153.550 4058 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.31 % Allowed : 13.05 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.30), residues: 761 helix: 2.81 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 67 TYR 0.045 0.002 TYR D 80 PHE 0.009 0.001 PHE B 61 HIS 0.004 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (12924) covalent geometry : angle 0.58309 / 0.34 (18715) hydrogen bonds : bond 0.04027 / 2.77 ( 780) hydrogen bonds : angle 2.57584 / 1.81 ( 1955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.60 seconds wall clock time: 51 minutes 8.05 seconds (3068.05 seconds total)