Starting phenix.real_space_refine on Fri Jul 3 02:16:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kb5_37070/07_2026/8kb5_37070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kb5_37070/07_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_37070/07_2026/8kb5_37070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kb5_37070/07_2026/8kb5_37070.map" model { file = "/net/cci-nas-00/data/ceres_data/8kb5_37070/07_2026/8kb5_37070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kb5_37070/07_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-dev-6108/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: 2.33, per 1000 atoms: 0.19 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: 0.94 Conformation dependent library (CDL) restraints added in 231.6 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: 1.67 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: 2.26 Time building geometry restraints manager: 1.27 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: 16493 1.68 - 3.35: 1705 3.35 - 5.03: 227 5.03 - 6.71: 42 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.990 Find NCS groups from input model: 0.120 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- 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= 0.748 Angle : 1.056 8.383 18479 Z= 0.915 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 1.05594 / 0.91 (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 : 0.243 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: 1.0647 time to fit residues: 176.7489 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 : 0.311 ------------------------------------------------------------------------------- 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: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.166439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126474 restraints weight = 10120.381| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 0.93 r_work: 0.3233 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12758 Z= 0.167 Angle : 0.707 8.167 18479 Z= 0.407 Chirality : 0.050 0.231 2104 Planarity : 0.005 0.042 1336 Dihedral : 30.704 74.115 4006 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.59 % Allowed : 13.54 % Favored : 84.87 % 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 (0.30), residues: 742 helix: 2.33 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.11 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 92 TYR 0.016 0.002 TYR F 51 PHE 0.012 0.002 PHE E 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 (12758) covalent geometry : angle 0.70736 / 0.41 (18479) hydrogen bonds : bond 0.05803 / 3.99 ( 782) hydrogen bonds : angle 3.09897 / 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 168 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.336 Fit side-chains REVERT: C 61 GLU cc_start: 0.8286 (tp30) cc_final: 0.8074 (tp30) REVERT: C 99 ARG cc_start: 0.7673 (mmt180) cc_final: 0.7194 (mmm160) REVERT: D 36 SER cc_start: 0.8473 (p) cc_final: 0.8240 (p) REVERT: G 15 LYS cc_start: 0.8106 (mtpm) cc_final: 0.7718 (mtmt) REVERT: H 51 ASP cc_start: 0.7929 (p0) cc_final: 0.7724 (OUTLIER) outliers start: 10 outliers final: 4 residues processed: 160 average time/residue: 1.0420 time to fit residues: 174.5931 Evaluate side-chains 156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 89 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN D 84 ASN F 93 GLN 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 = 0.3965 r_free = 0.3965 target = 0.163678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123098 restraints weight = 10128.545| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 0.93 r_work: 0.3199 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12758 Z= 0.210 Angle : 0.748 9.459 18479 Z= 0.421 Chirality : 0.053 0.242 2104 Planarity : 0.006 0.046 1336 Dihedral : 30.963 73.751 4006 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.59 % Allowed : 14.49 % 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: 2.46 (0.29), residues: 742 helix: 2.20 (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 0.005 0.001 ARG F 78 TYR 0.016 0.003 TYR F 51 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 0.00407 / 0.21 (12758) covalent geometry : angle 0.74848 / 0.42 (18479) hydrogen bonds : bond 0.06723 / 4.65 ( 782) hydrogen bonds : angle 3.12774 / 2.34 ( 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 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7662 (mmp-170) REVERT: C 61 GLU cc_start: 0.8274 (tp30) cc_final: 0.8047 (tp30) REVERT: C 99 ARG cc_start: 0.7728 (mmt180) cc_final: 0.7281 (mmm160) REVERT: G 15 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7732 (mtmt) outliers start: 10 outliers final: 4 residues processed: 159 average time/residue: 0.9531 time to fit residues: 158.8940 Evaluate side-chains 156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 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: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.164448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123979 restraints weight = 10161.037| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.92 r_work: 0.3215 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12758 Z= 0.174 Angle : 0.715 8.815 18479 Z= 0.404 Chirality : 0.050 0.234 2104 Planarity : 0.005 0.045 1336 Dihedral : 30.976 74.089 4006 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 2.57 (0.30), residues: 742 helix: 2.31 (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 0.004 0.000 ARG B 92 TYR 0.013 0.002 TYR F 51 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 0.00316 / 0.17 (12758) covalent geometry : angle 0.71461 / 0.40 (18479) hydrogen bonds : bond 0.06062 / 4.18 ( 782) hydrogen bonds : angle 3.09720 / 2.32 ( 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 163 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.299 Fit side-chains REVERT: B 92 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7563 (mmp-170) REVERT: C 61 GLU cc_start: 0.8256 (tp30) cc_final: 0.8042 (tp30) REVERT: C 99 ARG cc_start: 0.7731 (mmt180) cc_final: 0.7269 (mmm160) REVERT: E 86 ARG cc_start: 0.7837 (ttt-90) cc_final: 0.7574 (tpt170) REVERT: G 15 LYS cc_start: 0.8104 (mtpm) cc_final: 0.7725 (mtmt) outliers start: 9 outliers final: 4 residues processed: 157 average time/residue: 0.8826 time to fit residues: 145.2965 Evaluate side-chains 156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 72 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN 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 = 0.3991 r_free = 0.3991 target = 0.166147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125554 restraints weight = 10035.774| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 0.91 r_work: 0.3255 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12758 Z= 0.158 Angle : 0.671 7.887 18479 Z= 0.384 Chirality : 0.048 0.223 2104 Planarity : 0.005 0.043 1336 Dihedral : 30.951 74.691 4006 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 2.78 (0.30), residues: 742 helix: 2.55 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.20 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.021 0.002 TYR H 83 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (12758) covalent geometry : angle 0.67146 / 0.38 (18479) hydrogen bonds : bond 0.05584 / 3.85 ( 782) hydrogen bonds : angle 3.00282 / 2.25 ( 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 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.336 Fit side-chains REVERT: C 61 GLU cc_start: 0.8142 (tp30) cc_final: 0.7929 (tp30) REVERT: C 71 ARG cc_start: 0.7082 (ttm110) cc_final: 0.6850 (ttp80) REVERT: C 99 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7356 (mmm160) REVERT: E 59 GLU cc_start: 0.8500 (pm20) cc_final: 0.7972 (pm20) REVERT: G 15 LYS cc_start: 0.8048 (mtpm) cc_final: 0.7658 (mtmt) REVERT: G 99 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7755 (mmm160) outliers start: 11 outliers final: 5 residues processed: 159 average time/residue: 0.9376 time to fit residues: 156.3038 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 : 0.241 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.165011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125250 restraints weight = 10044.636| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.93 r_work: 0.3227 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12758 Z= 0.185 Angle : 0.705 8.943 18479 Z= 0.398 Chirality : 0.050 0.225 2104 Planarity : 0.005 0.045 1336 Dihedral : 31.042 74.022 4006 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 14.81 % 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: 2.62 (0.30), residues: 742 helix: 2.34 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.08 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 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 A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.19 (12758) covalent geometry : angle 0.70517 / 0.40 (18479) hydrogen bonds : bond 0.06165 / 4.27 ( 782) hydrogen bonds : angle 3.03336 / 2.26 ( 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 165 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.285 Fit side-chains REVERT: C 71 ARG cc_start: 0.7124 (ttm110) cc_final: 0.6902 (ttp80) REVERT: C 99 ARG cc_start: 0.7885 (mmt180) cc_final: 0.7408 (mmm160) REVERT: E 59 GLU cc_start: 0.8545 (pm20) cc_final: 0.8028 (pm20) REVERT: E 86 ARG cc_start: 0.7988 (ttt180) cc_final: 0.7760 (tpt170) REVERT: G 15 LYS cc_start: 0.8078 (mtpm) cc_final: 0.7698 (mtmt) REVERT: G 99 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7741 (mmm160) outliers start: 9 outliers final: 5 residues processed: 158 average time/residue: 0.8785 time to fit residues: 145.3968 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 : 0.184 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.165504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125825 restraints weight = 10001.418| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 0.92 r_work: 0.3237 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12758 Z= 0.165 Angle : 0.691 8.554 18479 Z= 0.391 Chirality : 0.049 0.225 2104 Planarity : 0.005 0.050 1336 Dihedral : 31.043 74.340 4006 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 15.29 % Favored : 83.28 % 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: 742 helix: 2.40 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.08 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.014 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 0.00297 / 0.16 (12758) covalent geometry : angle 0.69145 / 0.39 (18479) hydrogen bonds : bond 0.05867 / 4.05 ( 782) hydrogen bonds : angle 3.01787 / 2.26 ( 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 163 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: C 71 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6895 (ttp80) REVERT: C 99 ARG cc_start: 0.7766 (mmt180) cc_final: 0.7223 (mmm160) REVERT: E 59 GLU cc_start: 0.8475 (pm20) cc_final: 0.7969 (pm20) REVERT: E 86 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7670 (tpt170) REVERT: G 15 LYS cc_start: 0.8074 (mtpm) cc_final: 0.7693 (mtmt) outliers start: 9 outliers final: 6 residues processed: 158 average time/residue: 0.9121 time to fit residues: 150.9269 Evaluate side-chains 158 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 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 = 0.3989 r_free = 0.3989 target = 0.165937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126112 restraints weight = 10016.479| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.94 r_work: 0.3238 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12758 Z= 0.164 Angle : 0.680 8.177 18479 Z= 0.386 Chirality : 0.048 0.221 2104 Planarity : 0.005 0.054 1336 Dihedral : 31.025 74.689 4006 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.91 % Allowed : 14.49 % 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: 2.72 (0.30), residues: 742 helix: 2.41 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.06 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 79 TYR 0.016 0.002 TYR H 83 PHE 0.014 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12758) covalent geometry : angle 0.68009 / 0.39 (18479) hydrogen bonds : bond 0.05701 / 3.94 ( 782) hydrogen bonds : angle 2.99284 / 2.24 ( 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 165 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 71 ARG cc_start: 0.7109 (ttm110) cc_final: 0.6908 (ttp80) REVERT: C 99 ARG cc_start: 0.7752 (mmt180) cc_final: 0.7208 (mmm160) REVERT: E 59 GLU cc_start: 0.8468 (pm20) cc_final: 0.7961 (pm20) REVERT: E 86 ARG cc_start: 0.7926 (ttt180) cc_final: 0.7651 (tpt170) REVERT: G 15 LYS cc_start: 0.8050 (mtpm) cc_final: 0.7662 (mtmt) REVERT: G 77 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7637 (mtp180) REVERT: G 99 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7726 (mmm160) outliers start: 12 outliers final: 6 residues processed: 158 average time/residue: 0.9738 time to fit residues: 161.2262 Evaluate side-chains 159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 G residue 77 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 0.0970 chunk 73 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 39 optimal weight: 0.3980 chunk 86 optimal weight: 40.0000 chunk 14 optimal weight: 0.0000 chunk 24 optimal weight: 0.8980 overall best weight: 0.4782 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.167364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127994 restraints weight = 10022.056| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.92 r_work: 0.3268 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12758 Z= 0.138 Angle : 0.660 10.906 18479 Z= 0.376 Chirality : 0.046 0.216 2104 Planarity : 0.006 0.135 1336 Dihedral : 30.993 75.336 4006 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.59 % Allowed : 14.97 % 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: 2.89 (0.30), residues: 742 helix: 2.63 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.15 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.017 0.002 TYR H 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 0.00216 / 0.14 (12758) covalent geometry : angle 0.65969 / 0.38 (18479) hydrogen bonds : bond 0.05089 / 3.51 ( 782) hydrogen bonds : angle 2.97845 / 2.23 ( 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 164 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.310 Fit side-chains REVERT: C 71 ARG cc_start: 0.7090 (ttm110) cc_final: 0.6890 (ttp80) REVERT: C 99 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7161 (mmm160) REVERT: E 86 ARG cc_start: 0.7817 (ttt180) cc_final: 0.7546 (tpt170) REVERT: G 15 LYS cc_start: 0.8045 (mtpm) cc_final: 0.7649 (mtmt) REVERT: G 77 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7603 (mtp180) REVERT: G 99 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7722 (mmm160) outliers start: 10 outliers final: 6 residues processed: 157 average time/residue: 0.9537 time to fit residues: 156.9159 Evaluate side-chains 159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 77 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.163799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123641 restraints weight = 10046.651| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.95 r_work: 0.3211 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12758 Z= 0.247 Angle : 0.775 9.905 18479 Z= 0.428 Chirality : 0.054 0.232 2104 Planarity : 0.007 0.074 1336 Dihedral : 31.111 73.258 4006 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.59 % Allowed : 15.92 % 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: 2.38 (0.29), residues: 742 helix: 2.15 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.10 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 79 TYR 0.018 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 0.00508 / 0.25 (12758) covalent geometry : angle 0.77549 / 0.43 (18479) hydrogen bonds : bond 0.07077 / 4.89 ( 782) hydrogen bonds : angle 3.12013 / 2.33 ( 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 163 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.273 Fit side-chains REVERT: C 99 ARG cc_start: 0.7759 (mmt180) cc_final: 0.7197 (mmm160) REVERT: E 59 GLU cc_start: 0.8569 (pm20) cc_final: 0.8060 (pm20) REVERT: E 86 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7787 (tpt170) REVERT: G 15 LYS cc_start: 0.8104 (mtpm) cc_final: 0.7715 (mtmt) REVERT: G 77 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7720 (mtp180) REVERT: G 99 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7763 (mmm160) outliers start: 10 outliers final: 6 residues processed: 157 average time/residue: 1.0354 time to fit residues: 170.0445 Evaluate side-chains 159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 G residue 77 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 chunk 27 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.167260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127929 restraints weight = 10020.183| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.92 r_work: 0.3264 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12758 Z= 0.138 Angle : 0.668 7.517 18479 Z= 0.380 Chirality : 0.047 0.222 2104 Planarity : 0.006 0.099 1336 Dihedral : 31.074 75.541 4006 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.11 % Allowed : 16.56 % Favored : 82.32 % 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: 2.75 (0.30), residues: 742 helix: 2.52 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.019 0.002 TYR F 88 PHE 0.014 0.002 PHE E 67 HIS 0.003 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (12758) covalent geometry : angle 0.66788 / 0.38 (18479) hydrogen bonds : bond 0.05134 / 3.53 ( 782) hydrogen bonds : angle 3.02235 / 2.27 ( 1952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5743.40 seconds wall clock time: 97 minutes 53.92 seconds (5873.92 seconds total)