Starting phenix.real_space_refine on Wed Aug 5 20:12:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kb5_37070/08_2026/8kb5_37070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kb5_37070/08_2026/8kb5_37070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26133 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kb5_37070/08_2026/8kb5_37070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kb5_37070/08_2026/8kb5_37070.map" model { file = "/net/cci-nas-00/data/ceres_data/8kb5_37070/08_2026/8kb5_37070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kb5_37070/08_2026/8kb5_37070.cif" } resolution = 2.26133 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= 0.003 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 288 5.49 5 S 10 5.16 5 C 6610 2.51 5 N 2249 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11953 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2970 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.79, per 1000 atoms: 0.23 Number of scatterers: 11953 At special positions: 0 Unit cell: (117.66, 96.46, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2796 8.00 N 2249 7.00 C 6610 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: 1.01 Conformation dependent library (CDL) restraints added in 255.6 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.1% alpha, 2.9% beta 144 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.148A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.685A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.501A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.705A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) 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 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: 3.766A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.349A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.871A 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: 7.125A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.673A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.032A 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: 7.071A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 412 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 2.43 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: 2323 1.33 - 1.46: 4297 1.46 - 1.58: 5543 1.58 - 1.70: 577 1.70 - 1.82: 18 Bond restraints: 12758 Sorted by residual: bond pdb=" C5' DC J -27 " pdb=" C4' DC J -27 " ideal model delta sigma weight residual 1.512 1.557 -0.045 7.00e-03 2.04e+04 4.17e+01 bond pdb=" C5' DC I 55 " pdb=" C4' DC I 55 " ideal model delta sigma weight residual 1.512 1.555 -0.043 7.00e-03 2.04e+04 3.85e+01 bond pdb=" C5' DC J 37 " pdb=" C4' DC J 37 " ideal model delta sigma weight residual 1.512 1.551 -0.039 7.00e-03 2.04e+04 3.04e+01 bond pdb=" CA GLN F 93 " pdb=" C GLN F 93 " ideal model delta sigma weight residual 1.522 1.590 -0.068 1.38e-02 5.25e+03 2.43e+01 bond pdb=" C4 DC I -4 " pdb=" N4 DC I -4 " ideal model delta sigma weight residual 1.335 1.292 0.043 9.00e-03 1.23e+04 2.28e+01 ... (remaining 12753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 16472 1.68 - 3.35: 1712 3.35 - 5.03: 240 5.03 - 6.71: 43 6.71 - 8.38: 12 Bond angle restraints: 18479 Sorted by residual: angle pdb=" O5' DC I 55 " pdb=" C5' DC I 55 " pdb=" C4' DC I 55 " ideal model delta sigma weight residual 109.40 115.71 -6.31 8.00e-01 1.56e+00 6.22e+01 angle pdb=" O5' DC J 7 " pdb=" C5' DC J 7 " pdb=" C4' DC J 7 " ideal model delta sigma weight residual 109.40 114.28 -4.88 8.00e-01 1.56e+00 3.71e+01 angle pdb=" N GLN F 93 " pdb=" CA GLN F 93 " pdb=" C GLN F 93 " ideal model delta sigma weight residual 113.01 106.29 6.72 1.20e+00 6.94e-01 3.14e+01 angle pdb=" O5' DC I -46 " pdb=" C5' DC I -46 " pdb=" C4' DC I -46 " ideal model delta sigma weight residual 109.40 113.41 -4.01 8.00e-01 1.56e+00 2.51e+01 angle pdb=" O2 DC J 7 " pdb=" C2 DC J 7 " pdb=" N3 DC J 7 " ideal model delta sigma weight residual 121.90 118.40 3.50 7.00e-01 2.04e+00 2.50e+01 ... (remaining 18474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4327 17.62 - 35.24: 1141 35.24 - 52.86: 1073 52.86 - 70.48: 343 70.48 - 88.11: 16 Dihedral angle restraints: 6900 sinusoidal: 4712 harmonic: 2188 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " ideal model delta harmonic sigma weight residual 122.80 131.80 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1951 0.099 - 0.198: 142 0.198 - 0.297: 8 0.297 - 0.396: 2 0.396 - 0.495: 1 Chirality restraints: 2104 Sorted by residual: chirality pdb=" P DT I -17 " pdb=" OP1 DT I -17 " pdb=" OP2 DT I -17 " pdb=" O5' DT I -17 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C4' DC I 49 " pdb=" C5' DC I 49 " pdb=" O4' DC I 49 " pdb=" C3' DC I 49 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA GLN A 76 " pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CB GLN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 2101 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 56 " 0.119 2.00e-02 2.50e+03 6.39e-02 1.22e+02 pdb=" N9 DG J 56 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DG J 56 " -0.095 2.00e-02 2.50e+03 pdb=" N7 DG J 56 " -0.092 2.00e-02 2.50e+03 pdb=" C5 DG J 56 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DG J 56 " 0.041 2.00e-02 2.50e+03 pdb=" O6 DG J 56 " 0.088 2.00e-02 2.50e+03 pdb=" N1 DG J 56 " 0.030 2.00e-02 2.50e+03 pdb=" C2 DG J 56 " -0.022 2.00e-02 2.50e+03 pdb=" N2 DG J 56 " -0.069 2.00e-02 2.50e+03 pdb=" N3 DG J 56 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DG J 56 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -47 " 0.091 2.00e-02 2.50e+03 6.55e-02 1.07e+02 pdb=" N1 DT I -47 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DT I -47 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DT I -47 " -0.122 2.00e-02 2.50e+03 pdb=" N3 DT I -47 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DT I -47 " 0.026 2.00e-02 2.50e+03 pdb=" O4 DT I -47 " 0.092 2.00e-02 2.50e+03 pdb=" C5 DT I -47 " -0.028 2.00e-02 2.50e+03 pdb=" C7 DT I -47 " -0.086 2.00e-02 2.50e+03 pdb=" C6 DT I -47 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 59 " 0.120 2.00e-02 2.50e+03 6.05e-02 1.01e+02 pdb=" N9 DA I 59 " 0.007 2.00e-02 2.50e+03 pdb=" C8 DA I 59 " -0.070 2.00e-02 2.50e+03 pdb=" N7 DA I 59 " -0.062 2.00e-02 2.50e+03 pdb=" C5 DA I 59 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DA I 59 " 0.017 2.00e-02 2.50e+03 pdb=" N6 DA I 59 " 0.115 2.00e-02 2.50e+03 pdb=" N1 DA I 59 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DA I 59 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DA I 59 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DA I 59 " -0.017 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3664 2.88 - 3.39: 10210 3.39 - 3.89: 24290 3.89 - 4.40: 27833 4.40 - 4.90: 37547 Nonbonded interactions: 103544 Sorted by model distance: nonbonded pdb=" NE2 GLN E 125 " pdb=" OE2 GLU F 53 " model vdw 2.377 3.120 nonbonded pdb=" O ALA E 114 " pdb=" OG1 THR E 115 " model vdw 2.400 3.040 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.457 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.488 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NE ARG E 131 " model vdw 2.508 3.120 ... (remaining 103539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } 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: 1.100 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 0.071 12758 Z= 0.749 Angle : 1.065 8.383 18479 Z= 0.923 Chirality : 0.055 0.495 2104 Planarity : 0.013 0.111 1336 Dihedral : 28.085 88.105 5492 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.29), residues: 742 helix: 1.97 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 92 TYR 0.110 0.004 TYR F 51 PHE 0.029 0.003 PHE F 100 HIS 0.020 0.003 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.75 (12758) covalent geometry : angle 1.06506 / 0.92 (18479) hydrogen bonds : bond 0.11620 / 8.08 ( 782) hydrogen bonds : angle 3.68069 / 2.71 ( 1952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.331 Fit side-chains REVERT: C 61 GLU cc_start: 0.8294 (tp30) cc_final: 0.8077 (tp30) REVERT: C 99 ARG cc_start: 0.7357 (mmt180) cc_final: 0.7056 (mmm160) REVERT: D 36 SER cc_start: 0.8427 (p) cc_final: 0.8202 (p) REVERT: D 46 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8586 (mmmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.0856 time to fit residues: 180.6778 Evaluate side-chains 148 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN D 63 ASN D 84 ASN F 93 GLN G 24 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.167079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127456 restraints weight = 10130.461| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 0.94 r_work: 0.3243 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12758 Z= 0.157 Angle : 0.708 8.352 18479 Z= 0.405 Chirality : 0.050 0.237 2104 Planarity : 0.005 0.040 1336 Dihedral : 30.600 73.987 4006 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.27 % Allowed : 13.69 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.30), residues: 742 helix: 2.37 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.09 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 92 TYR 0.016 0.002 TYR F 51 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (12758) covalent geometry : angle 0.70772 / 0.41 (18479) hydrogen bonds : bond 0.05696 / 3.91 ( 782) hydrogen bonds : angle 3.09089 / 2.31 ( 1952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.337 Fit side-chains REVERT: A 39 HIS cc_start: 0.5837 (OUTLIER) cc_final: 0.5602 (p90) REVERT: C 61 GLU cc_start: 0.8278 (tp30) cc_final: 0.8056 (tp30) REVERT: C 99 ARG cc_start: 0.7652 (mmt180) cc_final: 0.7190 (mmm160) REVERT: D 36 SER cc_start: 0.8436 (p) cc_final: 0.8193 (p) REVERT: F 93 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8192 (mm110) REVERT: G 15 LYS cc_start: 0.8079 (mtpm) cc_final: 0.7695 (mtmt) REVERT: H 51 ASP cc_start: 0.7915 (p0) cc_final: 0.7711 (p0) outliers start: 8 outliers final: 1 residues processed: 160 average time/residue: 1.0685 time to fit residues: 179.1148 Evaluate side-chains 155 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain E residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123507 restraints weight = 10132.211| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 0.92 r_work: 0.3206 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12758 Z= 0.201 Angle : 0.752 9.316 18479 Z= 0.421 Chirality : 0.053 0.242 2104 Planarity : 0.006 0.045 1336 Dihedral : 30.836 73.568 4006 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.75 % Allowed : 14.49 % Favored : 83.76 % 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: 2.52 (0.29), residues: 742 helix: 2.25 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.08 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 78 TYR 0.015 0.003 TYR F 51 PHE 0.015 0.002 PHE E 67 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (12758) covalent geometry : angle 0.75244 / 0.42 (18479) hydrogen bonds : bond 0.06586 / 4.55 ( 782) hydrogen bonds : angle 3.11204 / 2.33 ( 1952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7659 (mmp-170) REVERT: C 61 GLU cc_start: 0.8281 (tp30) cc_final: 0.8053 (tp30) REVERT: C 99 ARG cc_start: 0.7746 (mmt180) cc_final: 0.7286 (mmm160) REVERT: F 79 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8833 (mtmt) REVERT: G 15 LYS cc_start: 0.8123 (mtpm) cc_final: 0.7729 (mtmt) outliers start: 11 outliers final: 4 residues processed: 160 average time/residue: 1.0228 time to fit residues: 171.5981 Evaluate side-chains 157 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 50.0000 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN C 112 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.164782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124297 restraints weight = 10158.724| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 0.93 r_work: 0.3218 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12758 Z= 0.169 Angle : 0.723 8.678 18479 Z= 0.406 Chirality : 0.051 0.235 2104 Planarity : 0.005 0.044 1336 Dihedral : 30.845 74.018 4006 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.43 % Allowed : 14.97 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.30), residues: 742 helix: 2.36 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.11 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.014 0.002 TYR F 51 PHE 0.014 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (12758) covalent geometry : angle 0.72346 / 0.41 (18479) hydrogen bonds : bond 0.05968 / 4.12 ( 782) hydrogen bonds : angle 3.08255 / 2.31 ( 1952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.322 Fit side-chains REVERT: C 61 GLU cc_start: 0.8249 (tp30) cc_final: 0.8034 (tp30) REVERT: C 99 ARG cc_start: 0.7732 (mmt180) cc_final: 0.7274 (mmm160) REVERT: E 86 ARG cc_start: 0.7835 (ttt-90) cc_final: 0.7605 (tpt170) REVERT: F 79 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8825 (mtmt) REVERT: G 15 LYS cc_start: 0.8099 (mtpm) cc_final: 0.7726 (mtmt) outliers start: 9 outliers final: 4 residues processed: 156 average time/residue: 1.0336 time to fit residues: 169.0078 Evaluate side-chains 155 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 112 GLN D 63 ASN D 84 ASN G 24 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124640 restraints weight = 10120.512| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.93 r_work: 0.3226 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12758 Z= 0.172 Angle : 0.714 8.309 18479 Z= 0.401 Chirality : 0.050 0.233 2104 Planarity : 0.005 0.049 1336 Dihedral : 30.853 74.176 4006 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.43 % Allowed : 14.65 % Favored : 83.92 % 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: 2.67 (0.30), residues: 742 helix: 2.38 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.09 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.016 0.002 TYR H 83 PHE 0.014 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (12758) covalent geometry : angle 0.71407 / 0.40 (18479) hydrogen bonds : bond 0.05918 / 4.09 ( 782) hydrogen bonds : angle 3.03933 / 2.27 ( 1952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.340 Fit side-chains REVERT: C 61 GLU cc_start: 0.8214 (tp30) cc_final: 0.8014 (tp30) REVERT: C 99 ARG cc_start: 0.7730 (mmt180) cc_final: 0.7268 (mmm160) REVERT: F 79 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8816 (mtmt) REVERT: G 15 LYS cc_start: 0.8096 (mtpm) cc_final: 0.7723 (mtmt) REVERT: G 99 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7825 (mmm160) outliers start: 9 outliers final: 5 residues processed: 155 average time/residue: 1.0515 time to fit residues: 170.7596 Evaluate side-chains 156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.164563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124934 restraints weight = 10036.808| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 0.89 r_work: 0.3217 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12758 Z= 0.197 Angle : 0.743 9.399 18479 Z= 0.412 Chirality : 0.052 0.231 2104 Planarity : 0.005 0.045 1336 Dihedral : 31.006 73.564 4006 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.75 % Allowed : 14.81 % Favored : 83.44 % 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 (0.29), residues: 742 helix: 2.25 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.12 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.019 0.003 TYR H 83 PHE 0.015 0.002 PHE E 67 HIS 0.006 0.002 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (12758) covalent geometry : angle 0.74320 / 0.41 (18479) hydrogen bonds : bond 0.06449 / 4.45 ( 782) hydrogen bonds : angle 3.07810 / 2.30 ( 1952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.338 Fit side-chains REVERT: C 71 ARG cc_start: 0.7284 (ttm110) cc_final: 0.7072 (ttp80) REVERT: C 99 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7325 (mmm160) REVERT: E 59 GLU cc_start: 0.8558 (pm20) cc_final: 0.8044 (pm20) REVERT: E 64 LYS cc_start: 0.8624 (mtpm) cc_final: 0.8243 (mppt) REVERT: F 79 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8762 (mtmt) REVERT: G 15 LYS cc_start: 0.8098 (mtpm) cc_final: 0.7708 (mtmt) outliers start: 11 outliers final: 5 residues processed: 159 average time/residue: 1.0394 time to fit residues: 173.2119 Evaluate side-chains 156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 104 GLN C 112 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125562 restraints weight = 9998.427| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 0.92 r_work: 0.3231 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12758 Z= 0.166 Angle : 0.722 8.811 18479 Z= 0.402 Chirality : 0.050 0.231 2104 Planarity : 0.005 0.053 1336 Dihedral : 31.002 74.010 4006 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.75 % Allowed : 15.13 % Favored : 83.12 % 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: 2.60 (0.29), residues: 742 helix: 2.33 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.13 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.015 0.002 TYR H 83 PHE 0.015 0.002 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (12758) covalent geometry : angle 0.72180 / 0.40 (18479) hydrogen bonds : bond 0.05989 / 4.14 ( 782) hydrogen bonds : angle 3.05254 / 2.28 ( 1952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.344 Fit side-chains REVERT: C 99 ARG cc_start: 0.7754 (mmt180) cc_final: 0.7215 (mmm160) REVERT: E 59 GLU cc_start: 0.8537 (pm20) cc_final: 0.8036 (pm20) REVERT: E 64 LYS cc_start: 0.8598 (mtpm) cc_final: 0.8219 (mppt) REVERT: F 79 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8754 (mtmt) REVERT: G 15 LYS cc_start: 0.8099 (mtpm) cc_final: 0.7704 (mtmt) REVERT: G 99 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7719 (mmm160) outliers start: 11 outliers final: 6 residues processed: 157 average time/residue: 1.0366 time to fit residues: 170.5448 Evaluate side-chains 158 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 0.0020 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 73 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127493 restraints weight = 10039.082| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.93 r_work: 0.3258 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 12758 Z= 0.139 Angle : 0.695 10.901 18479 Z= 0.389 Chirality : 0.048 0.224 2104 Planarity : 0.005 0.073 1336 Dihedral : 30.955 74.927 4006 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.59 % Allowed : 15.45 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.30), residues: 742 helix: 2.47 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.07 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 71 TYR 0.019 0.002 TYR D 83 PHE 0.014 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.14 (12758) covalent geometry : angle 0.69524 / 0.39 (18479) hydrogen bonds : bond 0.05236 / 3.61 ( 782) hydrogen bonds : angle 3.01759 / 2.26 ( 1952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: C 99 ARG cc_start: 0.7737 (mmt180) cc_final: 0.7192 (mmm160) REVERT: E 59 GLU cc_start: 0.8467 (pm20) cc_final: 0.7967 (pm20) REVERT: E 64 LYS cc_start: 0.8545 (mtpm) cc_final: 0.8163 (mppt) REVERT: F 79 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8741 (mtmt) REVERT: G 15 LYS cc_start: 0.8047 (mtpm) cc_final: 0.7666 (mtmt) outliers start: 10 outliers final: 5 residues processed: 156 average time/residue: 1.0553 time to fit residues: 172.6296 Evaluate side-chains 156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.0670 chunk 91 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 40.0000 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN E 125 GLN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128295 restraints weight = 10036.508| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 0.97 r_work: 0.3254 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12758 Z= 0.142 Angle : 0.648 7.539 18479 Z= 0.370 Chirality : 0.046 0.222 2104 Planarity : 0.004 0.040 1336 Dihedral : 30.794 75.265 4006 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.43 % Allowed : 15.45 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.30), residues: 742 helix: 2.71 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.13 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 71 TYR 0.014 0.002 TYR H 83 PHE 0.013 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (12758) covalent geometry : angle 0.64776 / 0.37 (18479) hydrogen bonds : bond 0.05109 / 3.52 ( 782) hydrogen bonds : angle 2.91138 / 2.17 ( 1952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.326 Fit side-chains REVERT: C 99 ARG cc_start: 0.7754 (mmt180) cc_final: 0.7147 (mmm160) REVERT: E 64 LYS cc_start: 0.8548 (mtpm) cc_final: 0.8139 (mppt) REVERT: F 79 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8750 (mtmt) REVERT: G 15 LYS cc_start: 0.8051 (mtpm) cc_final: 0.7647 (mtmt) REVERT: G 77 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7675 (mtp180) outliers start: 9 outliers final: 4 residues processed: 158 average time/residue: 1.0389 time to fit residues: 171.9774 Evaluate side-chains 156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 70 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 23 optimal weight: 0.1980 chunk 77 optimal weight: 9.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN E 68 GLN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.163811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123765 restraints weight = 10039.690| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 0.94 r_work: 0.3207 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12758 Z= 0.246 Angle : 0.796 10.536 18479 Z= 0.433 Chirality : 0.055 0.234 2104 Planarity : 0.006 0.060 1336 Dihedral : 31.022 73.093 4006 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.43 % Allowed : 15.92 % Favored : 82.64 % 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: 2.34 (0.29), residues: 742 helix: 2.12 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.12 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 79 TYR 0.020 0.003 TYR F 88 PHE 0.015 0.003 PHE E 67 HIS 0.007 0.002 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 (12758) covalent geometry : angle 0.79635 / 0.43 (18479) hydrogen bonds : bond 0.07171 / 4.96 ( 782) hydrogen bonds : angle 3.13779 / 2.34 ( 1952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.209 Fit side-chains REVERT: C 99 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7190 (mmm160) REVERT: E 59 GLU cc_start: 0.8573 (pm20) cc_final: 0.8045 (pm20) REVERT: E 64 LYS cc_start: 0.8628 (mtpm) cc_final: 0.8272 (mppt) REVERT: F 79 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8723 (mtmm) REVERT: G 15 LYS cc_start: 0.8127 (mtpm) cc_final: 0.7726 (mtmt) REVERT: G 77 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7728 (mtp180) outliers start: 9 outliers final: 4 residues processed: 155 average time/residue: 0.9148 time to fit residues: 148.4409 Evaluate side-chains 155 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127248 restraints weight = 9983.442| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.93 r_work: 0.3236 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12758 Z= 0.144 Angle : 0.698 8.364 18479 Z= 0.390 Chirality : 0.049 0.228 2104 Planarity : 0.005 0.061 1336 Dihedral : 30.999 74.981 4006 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.27 % Allowed : 16.24 % Favored : 82.48 % 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: 2.61 (0.29), residues: 742 helix: 2.43 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 39 TYR 0.018 0.002 TYR F 88 PHE 0.016 0.002 PHE E 67 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12758) covalent geometry : angle 0.69837 / 0.39 (18479) hydrogen bonds : bond 0.05348 / 3.68 ( 782) hydrogen bonds : angle 3.08411 / 2.31 ( 1952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6213.97 seconds wall clock time: 106 minutes 2.32 seconds (6362.32 seconds total)