Starting phenix.real_space_refine on Thu Jul 2 11:29:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etv_28600/07_2026/8etv_28600_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etv_28600/07_2026/8etv_28600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8etv_28600/07_2026/8etv_28600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etv_28600/07_2026/8etv_28600.map" model { file = "/net/cci-nas-00/data/ceres_data/8etv_28600/07_2026/8etv_28600_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etv_28600/07_2026/8etv_28600_neut.cif" } resolution = 3.16 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= 0.011 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 218 5.49 5 S 8 5.16 5 C 4769 2.51 5 N 1634 2.21 5 O 2053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 8682 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2240 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2264 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Time building chain proxies: 1.89, per 1000 atoms: 0.22 Number of scatterers: 8682 At special positions: 0 Unit cell: (117.735, 103.54, 105.21, 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 8 16.00 P 218 15.00 O 2053 8.00 N 1634 7.00 C 4769 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: 0.71 Conformation dependent library (CDL) restraints added in 347.3 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 75.8% alpha, 2.7% beta 108 base pairs and 192 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.541A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.546A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.844A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.034A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.666A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.139A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.559A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.382A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.532A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.772A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.560A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.860A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.625A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.541A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.299A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.619A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.311A 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 'C' and resid 42 through 43 removed outlier: 7.380A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.406A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.762A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 278 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 192 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.00 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: 1737 1.33 - 1.45: 3088 1.45 - 1.57: 4005 1.57 - 1.69: 436 1.69 - 1.81: 16 Bond restraints: 9282 Sorted by residual: bond pdb=" C5' DA I -35 " pdb=" C4' DA I -35 " ideal model delta sigma weight residual 1.512 1.542 -0.030 7.00e-03 2.04e+04 1.85e+01 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DC J -25 " pdb=" C2' DC J -25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 13298 2.90 - 5.80: 153 5.80 - 8.70: 21 8.70 - 11.60: 3 11.60 - 14.50: 2 Bond angle restraints: 13477 Sorted by residual: angle pdb=" O4' DG I 25 " pdb=" C1' DG I 25 " pdb=" N9 DG I 25 " ideal model delta sigma weight residual 108.00 112.35 -4.35 7.00e-01 2.04e+00 3.86e+01 angle pdb=" N GLU C 61 " pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " ideal model delta sigma weight residual 110.12 118.88 -8.76 1.47e+00 4.63e-01 3.55e+01 angle pdb=" O5' DA I -35 " pdb=" C5' DA I -35 " pdb=" C4' DA I -35 " ideal model delta sigma weight residual 109.40 113.97 -4.57 8.00e-01 1.56e+00 3.26e+01 angle pdb=" O5' DA I -54 " pdb=" C5' DA I -54 " pdb=" C4' DA I -54 " ideal model delta sigma weight residual 109.40 113.37 -3.97 8.00e-01 1.56e+00 2.46e+01 angle pdb=" CB MET D 56 " pdb=" CG MET D 56 " pdb=" SD MET D 56 " ideal model delta sigma weight residual 112.70 127.20 -14.50 3.00e+00 1.11e-01 2.34e+01 ... (remaining 13472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 3935 35.02 - 70.04: 1052 70.04 - 105.07: 14 105.07 - 140.09: 0 140.09 - 175.11: 2 Dihedral angle restraints: 5003 sinusoidal: 3480 harmonic: 1523 Sorted by residual: dihedral pdb=" CA LYS F 77 " pdb=" C LYS F 77 " pdb=" N ARG F 78 " pdb=" CA ARG F 78 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ILE F 50 " pdb=" C ILE F 50 " pdb=" N TYR F 51 " pdb=" CA TYR F 51 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.11 -175.11 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1233 0.071 - 0.142: 281 0.142 - 0.213: 18 0.213 - 0.284: 3 0.284 - 0.354: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1533 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO C 80 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -54 " -0.032 2.00e-02 2.50e+03 1.46e-02 5.84e+00 pdb=" N9 DA I -54 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DA I -54 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -54 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I -54 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I -54 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I -54 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -54 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -54 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -54 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " -0.023 2.00e-02 2.50e+03 1.69e-02 5.74e+00 pdb=" CG TYR D 80 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2066 2.82 - 3.34: 7286 3.34 - 3.86: 17089 3.86 - 4.38: 19200 4.38 - 4.90: 26702 Nonbonded interactions: 72343 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 48 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR B 30 " pdb=" OP1 DC I -12 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.346 3.040 nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.366 3.120 ... (remaining 72338 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 'B' and resid 24 through 94) selection = (chain 'F' and resid 24 through 94) } 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: 10.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 0.066 9282 Z= 0.660 Angle : 1.002 14.501 13477 Z= 0.795 Chirality : 0.057 0.354 1536 Planarity : 0.008 0.083 944 Dihedral : 28.214 175.111 4017 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.33), residues: 512 helix: -0.35 (0.24), residues: 373 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 45 TYR 0.039 0.004 TYR D 80 PHE 0.016 0.003 PHE E 84 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.66 ( 9282) covalent geometry : angle 1.00219 / 0.80 (13477) hydrogen bonds : bond 0.11601 / 7.66 ( 559) hydrogen bonds : angle 3.96683 / 2.81 ( 1378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8711 (mm) cc_final: 0.8504 (mm) REVERT: A 125 GLN cc_start: 0.7609 (mp10) cc_final: 0.7356 (mp10) REVERT: B 36 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: B 66 ILE cc_start: 0.8802 (mm) cc_final: 0.8581 (tp) REVERT: B 73 THR cc_start: 0.8696 (m) cc_final: 0.8432 (m) REVERT: B 81 VAL cc_start: 0.8703 (t) cc_final: 0.8437 (t) REVERT: B 82 THR cc_start: 0.8609 (t) cc_final: 0.8055 (p) REVERT: B 88 TYR cc_start: 0.7286 (m-80) cc_final: 0.6780 (m-80) REVERT: B 91 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7925 (mtmm) REVERT: C 17 ARG cc_start: 0.7434 (ptm160) cc_final: 0.6956 (ptm160) REVERT: C 64 GLU cc_start: 0.7762 (tp30) cc_final: 0.7316 (tp30) REVERT: C 68 ASN cc_start: 0.8034 (m-40) cc_final: 0.6703 (m-40) REVERT: C 72 ASP cc_start: 0.7911 (m-30) cc_final: 0.7525 (m-30) REVERT: C 73 ASN cc_start: 0.8115 (t160) cc_final: 0.7804 (t0) REVERT: C 81 ARG cc_start: 0.7909 (tpt170) cc_final: 0.7549 (tpt170) REVERT: C 99 ARG cc_start: 0.6990 (mpt180) cc_final: 0.6750 (mpt180) REVERT: D 43 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8387 (mmmm) REVERT: D 54 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8509 (mmmm) REVERT: D 60 ASN cc_start: 0.8471 (t0) cc_final: 0.8212 (t0) REVERT: D 69 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8523 (mtp180) REVERT: E 59 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6670 (tm-30) REVERT: E 60 LEU cc_start: 0.7951 (mt) cc_final: 0.7077 (mt) REVERT: E 68 GLN cc_start: 0.7923 (tt0) cc_final: 0.7698 (tt0) REVERT: E 69 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7795 (ttm110) REVERT: E 92 LEU cc_start: 0.8634 (mt) cc_final: 0.8412 (mt) REVERT: E 96 SER cc_start: 0.8310 (m) cc_final: 0.8067 (m) REVERT: F 26 ILE cc_start: 0.8937 (tp) cc_final: 0.8690 (tt) REVERT: F 36 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7214 (mtm-85) REVERT: F 88 TYR cc_start: 0.8081 (m-80) cc_final: 0.7820 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1579 time to fit residues: 43.1457 Evaluate side-chains 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 84 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.103735 restraints weight = 16699.957| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.07 r_work: 0.3421 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 9282 Z= 0.406 Angle : 0.867 12.180 13477 Z= 0.497 Chirality : 0.054 0.230 1536 Planarity : 0.007 0.065 944 Dihedral : 31.518 173.954 2968 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.89 % Allowed : 16.70 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.34), residues: 512 helix: 0.76 (0.25), residues: 370 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 77 TYR 0.040 0.004 TYR B 88 PHE 0.013 0.003 PHE D 67 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.41 ( 9282) covalent geometry : angle 0.86710 / 0.50 (13477) hydrogen bonds : bond 0.08379 / 5.66 ( 559) hydrogen bonds : angle 3.69723 / 2.68 ( 1378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7978 (ttp-110) REVERT: B 27 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8185 (mp10) REVERT: B 82 THR cc_start: 0.8700 (t) cc_final: 0.8216 (p) REVERT: B 91 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8491 (mtmm) REVERT: C 17 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7508 (ptm160) REVERT: C 57 TYR cc_start: 0.8362 (t80) cc_final: 0.7592 (t80) REVERT: C 61 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: C 64 GLU cc_start: 0.8371 (tp30) cc_final: 0.8153 (tp30) REVERT: C 68 ASN cc_start: 0.8372 (m-40) cc_final: 0.7407 (m110) REVERT: C 72 ASP cc_start: 0.8442 (m-30) cc_final: 0.8171 (m-30) REVERT: C 77 ARG cc_start: 0.7141 (ttm110) cc_final: 0.6854 (ttm110) REVERT: C 99 ARG cc_start: 0.8188 (mpt180) cc_final: 0.7890 (mpt180) REVERT: D 39 TYR cc_start: 0.8419 (t80) cc_final: 0.8176 (t80) REVERT: D 43 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8726 (mmmm) REVERT: D 44 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 60 ASN cc_start: 0.8733 (t0) cc_final: 0.8514 (t0) REVERT: D 69 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8582 (mtp180) REVERT: E 99 TYR cc_start: 0.8330 (t80) cc_final: 0.8084 (t80) REVERT: E 129 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8388 (mmm-85) REVERT: F 88 TYR cc_start: 0.8577 (m-80) cc_final: 0.7909 (m-80) REVERT: F 91 LYS cc_start: 0.8256 (mtmt) cc_final: 0.8030 (mtmt) outliers start: 17 outliers final: 11 residues processed: 242 average time/residue: 0.1539 time to fit residues: 45.4221 Evaluate side-chains 252 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN E 68 GLN E 108 ASN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.131272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107417 restraints weight = 16421.867| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.94 r_work: 0.3484 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9282 Z= 0.186 Angle : 0.678 10.471 13477 Z= 0.406 Chirality : 0.045 0.209 1536 Planarity : 0.005 0.060 944 Dihedral : 31.535 174.485 2968 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.03 % Allowed : 23.34 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.36), residues: 512 helix: 1.60 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.84 (0.47), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.030 0.003 TYR B 88 PHE 0.010 0.002 PHE E 78 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.19 ( 9282) covalent geometry : angle 0.67828 / 0.41 (13477) hydrogen bonds : bond 0.06028 / 4.07 ( 559) hydrogen bonds : angle 3.20836 / 2.31 ( 1378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8540 (tp) cc_final: 0.8284 (tt) REVERT: B 45 ARG cc_start: 0.8278 (tpp80) cc_final: 0.8064 (tpp80) REVERT: B 82 THR cc_start: 0.8707 (t) cc_final: 0.8272 (p) REVERT: B 88 TYR cc_start: 0.8009 (m-80) cc_final: 0.7626 (m-80) REVERT: B 91 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8381 (mttm) REVERT: C 17 ARG cc_start: 0.7950 (ptm160) cc_final: 0.7420 (ptm160) REVERT: C 57 TYR cc_start: 0.8215 (t80) cc_final: 0.7461 (t80) REVERT: C 61 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: C 64 GLU cc_start: 0.8289 (tp30) cc_final: 0.8004 (tp30) REVERT: C 68 ASN cc_start: 0.8215 (m-40) cc_final: 0.7129 (m110) REVERT: C 72 ASP cc_start: 0.8330 (m-30) cc_final: 0.7969 (m-30) REVERT: C 77 ARG cc_start: 0.7012 (ttm110) cc_final: 0.6776 (ttm110) REVERT: C 99 ARG cc_start: 0.8118 (mpt180) cc_final: 0.7799 (mpt180) REVERT: D 39 TYR cc_start: 0.8304 (t80) cc_final: 0.7907 (t80) REVERT: D 43 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8687 (mmmm) REVERT: D 44 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 60 ASN cc_start: 0.8691 (t0) cc_final: 0.8472 (t0) REVERT: D 65 ASP cc_start: 0.8076 (t0) cc_final: 0.7848 (t0) REVERT: D 69 ARG cc_start: 0.8835 (ttm170) cc_final: 0.8549 (mtp180) REVERT: E 120 MET cc_start: 0.7525 (mtp) cc_final: 0.7224 (mtp) REVERT: E 129 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8355 (mmm-85) REVERT: F 88 TYR cc_start: 0.8486 (m-80) cc_final: 0.8234 (m-80) outliers start: 22 outliers final: 14 residues processed: 234 average time/residue: 0.1561 time to fit residues: 44.5532 Evaluate side-chains 248 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN E 108 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.130263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.106139 restraints weight = 16733.421| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.97 r_work: 0.3469 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9282 Z= 0.218 Angle : 0.686 11.795 13477 Z= 0.405 Chirality : 0.044 0.205 1536 Planarity : 0.005 0.059 944 Dihedral : 31.547 174.095 2968 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.86 % Allowed : 23.11 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.36), residues: 512 helix: 1.73 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.89 (0.48), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.023 0.003 TYR B 88 PHE 0.010 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.22 ( 9282) covalent geometry : angle 0.68585 / 0.41 (13477) hydrogen bonds : bond 0.06083 / 4.10 ( 559) hydrogen bonds : angle 3.26510 / 2.35 ( 1378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8555 (tp) cc_final: 0.8288 (tt) REVERT: A 125 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: B 45 ARG cc_start: 0.8282 (tpp80) cc_final: 0.8065 (tpp80) REVERT: B 82 THR cc_start: 0.8707 (t) cc_final: 0.8293 (p) REVERT: B 88 TYR cc_start: 0.7954 (m-80) cc_final: 0.7715 (m-80) REVERT: C 17 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7441 (ptm160) REVERT: C 24 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8257 (mm110) REVERT: C 42 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7875 (mtm-85) REVERT: C 56 GLU cc_start: 0.8186 (tp30) cc_final: 0.7700 (tp30) REVERT: C 64 GLU cc_start: 0.8255 (tp30) cc_final: 0.8028 (tp30) REVERT: C 68 ASN cc_start: 0.8206 (m-40) cc_final: 0.7175 (m-40) REVERT: C 72 ASP cc_start: 0.8345 (m-30) cc_final: 0.7982 (m-30) REVERT: C 99 ARG cc_start: 0.8135 (mpt180) cc_final: 0.7810 (mpt180) REVERT: D 39 TYR cc_start: 0.8389 (t80) cc_final: 0.8042 (t80) REVERT: D 43 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8654 (mmmm) REVERT: D 44 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8477 (tm-30) REVERT: D 60 ASN cc_start: 0.8699 (t0) cc_final: 0.8467 (t0) REVERT: D 65 ASP cc_start: 0.8066 (t0) cc_final: 0.7789 (t0) REVERT: D 69 ARG cc_start: 0.8842 (ttm170) cc_final: 0.8565 (mtp180) REVERT: E 120 MET cc_start: 0.7563 (mtp) cc_final: 0.7265 (mtp) REVERT: E 129 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8319 (mtp85) REVERT: F 87 VAL cc_start: 0.9214 (t) cc_final: 0.8775 (t) REVERT: F 88 TYR cc_start: 0.8518 (m-80) cc_final: 0.7948 (m-80) REVERT: F 91 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7963 (mtmt) outliers start: 30 outliers final: 25 residues processed: 233 average time/residue: 0.1564 time to fit residues: 44.6279 Evaluate side-chains 255 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.130536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106437 restraints weight = 16713.643| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.96 r_work: 0.3473 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9282 Z= 0.200 Angle : 0.666 12.030 13477 Z= 0.396 Chirality : 0.044 0.207 1536 Planarity : 0.005 0.057 944 Dihedral : 31.541 173.395 2968 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.86 % Allowed : 23.34 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.37), residues: 512 helix: 1.85 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.78 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 77 TYR 0.018 0.002 TYR B 72 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.20 ( 9282) covalent geometry : angle 0.66608 / 0.40 (13477) hydrogen bonds : bond 0.05820 / 3.92 ( 559) hydrogen bonds : angle 3.21722 / 2.31 ( 1378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8557 (tp) cc_final: 0.8267 (tt) REVERT: A 125 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: A 128 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8234 (mtm-85) REVERT: B 67 ARG cc_start: 0.8340 (ttm170) cc_final: 0.8022 (ttm-80) REVERT: C 17 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7432 (ptm160) REVERT: C 24 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8300 (mm110) REVERT: C 42 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7928 (mtm-85) REVERT: C 56 GLU cc_start: 0.8159 (tp30) cc_final: 0.7673 (tp30) REVERT: C 57 TYR cc_start: 0.8222 (t80) cc_final: 0.7336 (t80) REVERT: C 61 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: C 64 GLU cc_start: 0.8259 (tp30) cc_final: 0.7924 (tp30) REVERT: C 68 ASN cc_start: 0.8164 (m-40) cc_final: 0.7086 (m-40) REVERT: C 72 ASP cc_start: 0.8344 (m-30) cc_final: 0.7980 (m-30) REVERT: C 99 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7799 (mpt180) REVERT: D 39 TYR cc_start: 0.8363 (t80) cc_final: 0.8052 (t80) REVERT: D 43 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8651 (mmmm) REVERT: D 44 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8484 (tm-30) REVERT: D 60 ASN cc_start: 0.8664 (t0) cc_final: 0.8453 (t0) REVERT: D 65 ASP cc_start: 0.8068 (t0) cc_final: 0.7785 (t0) REVERT: D 69 ARG cc_start: 0.8836 (ttm170) cc_final: 0.8539 (mtp180) REVERT: E 120 MET cc_start: 0.7505 (mtp) cc_final: 0.7214 (mtp) REVERT: E 129 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8340 (tmm-80) REVERT: F 88 TYR cc_start: 0.8511 (m-80) cc_final: 0.7947 (m-80) REVERT: F 91 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7949 (mtmt) outliers start: 30 outliers final: 25 residues processed: 232 average time/residue: 0.1451 time to fit residues: 41.4398 Evaluate side-chains 256 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.130772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106861 restraints weight = 16731.393| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.95 r_work: 0.3480 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9282 Z= 0.189 Angle : 0.660 10.934 13477 Z= 0.392 Chirality : 0.043 0.208 1536 Planarity : 0.005 0.057 944 Dihedral : 31.508 173.056 2968 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.86 % Allowed : 24.71 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.36), residues: 512 helix: 1.92 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.78 (0.48), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 55 TYR 0.025 0.002 TYR B 88 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 ( 9282) covalent geometry : angle 0.65956 / 0.39 (13477) hydrogen bonds : bond 0.05701 / 3.83 ( 559) hydrogen bonds : angle 3.21150 / 2.30 ( 1378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8561 (tp) cc_final: 0.8270 (tt) REVERT: A 125 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: B 67 ARG cc_start: 0.8345 (ttm170) cc_final: 0.8037 (ttm-80) REVERT: B 88 TYR cc_start: 0.7941 (m-80) cc_final: 0.7677 (m-80) REVERT: B 91 LYS cc_start: 0.8638 (mttm) cc_final: 0.8436 (mtmm) REVERT: C 17 ARG cc_start: 0.7969 (ptm160) cc_final: 0.7437 (ptm160) REVERT: C 24 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8295 (mm110) REVERT: C 42 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7920 (mtm-85) REVERT: C 56 GLU cc_start: 0.8163 (tp30) cc_final: 0.7656 (tp30) REVERT: C 57 TYR cc_start: 0.8181 (t80) cc_final: 0.7959 (t80) REVERT: C 64 GLU cc_start: 0.8236 (tp30) cc_final: 0.7902 (tp30) REVERT: C 68 ASN cc_start: 0.8169 (m-40) cc_final: 0.7090 (m-40) REVERT: C 72 ASP cc_start: 0.8322 (m-30) cc_final: 0.7948 (m-30) REVERT: C 99 ARG cc_start: 0.8099 (mpt180) cc_final: 0.7770 (mpt180) REVERT: D 39 TYR cc_start: 0.8349 (t80) cc_final: 0.8051 (t80) REVERT: D 43 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8640 (mmmm) REVERT: D 44 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 60 ASN cc_start: 0.8649 (t0) cc_final: 0.8437 (t0) REVERT: D 65 ASP cc_start: 0.8065 (t0) cc_final: 0.7777 (t0) REVERT: D 69 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8524 (mtp180) REVERT: E 120 MET cc_start: 0.7488 (mtp) cc_final: 0.7212 (mtp) REVERT: F 87 VAL cc_start: 0.9217 (t) cc_final: 0.8790 (t) REVERT: F 88 TYR cc_start: 0.8491 (m-80) cc_final: 0.7940 (m-80) REVERT: F 91 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7943 (mtmt) outliers start: 30 outliers final: 24 residues processed: 231 average time/residue: 0.1277 time to fit residues: 36.4708 Evaluate side-chains 254 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 108 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.130383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106363 restraints weight = 16848.976| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.97 r_work: 0.3474 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9282 Z= 0.200 Angle : 0.661 13.185 13477 Z= 0.393 Chirality : 0.043 0.209 1536 Planarity : 0.005 0.060 944 Dihedral : 31.437 172.465 2968 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 7.55 % Allowed : 24.71 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.36), residues: 512 helix: 1.91 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.77 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 55 TYR 0.020 0.002 TYR F 51 PHE 0.010 0.002 PHE F 61 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.20 ( 9282) covalent geometry : angle 0.66134 / 0.39 (13477) hydrogen bonds : bond 0.05766 / 3.88 ( 559) hydrogen bonds : angle 3.22999 / 2.32 ( 1378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8596 (tp) cc_final: 0.8312 (tt) REVERT: A 125 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: A 128 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8214 (mmm-85) REVERT: B 67 ARG cc_start: 0.8377 (ttm170) cc_final: 0.8062 (ttm-80) REVERT: B 88 TYR cc_start: 0.7981 (m-80) cc_final: 0.7651 (m-80) REVERT: B 91 LYS cc_start: 0.8652 (mttm) cc_final: 0.8414 (mtmm) REVERT: C 17 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7426 (ptm160) REVERT: C 56 GLU cc_start: 0.8240 (tp30) cc_final: 0.7716 (tp30) REVERT: C 57 TYR cc_start: 0.8101 (t80) cc_final: 0.7758 (t80) REVERT: C 64 GLU cc_start: 0.8202 (tp30) cc_final: 0.7865 (tp30) REVERT: C 68 ASN cc_start: 0.8137 (m-40) cc_final: 0.7052 (m-40) REVERT: C 72 ASP cc_start: 0.8345 (m-30) cc_final: 0.7971 (m-30) REVERT: C 99 ARG cc_start: 0.8096 (mpt180) cc_final: 0.7758 (mpt180) REVERT: D 39 TYR cc_start: 0.8379 (t80) cc_final: 0.8083 (t80) REVERT: D 43 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8627 (mmmm) REVERT: D 44 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8498 (tm-30) REVERT: D 60 ASN cc_start: 0.8657 (t0) cc_final: 0.8448 (t0) REVERT: D 65 ASP cc_start: 0.8077 (t0) cc_final: 0.7793 (t0) REVERT: D 69 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8522 (mtp180) REVERT: F 87 VAL cc_start: 0.9225 (t) cc_final: 0.8815 (t) REVERT: F 88 TYR cc_start: 0.8496 (m-80) cc_final: 0.7949 (m-80) REVERT: F 91 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7959 (mtmt) outliers start: 33 outliers final: 22 residues processed: 231 average time/residue: 0.1349 time to fit residues: 38.4838 Evaluate side-chains 249 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 31 HIS D 79 HIS E 108 ASN F 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.131239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107523 restraints weight = 16687.796| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.95 r_work: 0.3486 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9282 Z= 0.184 Angle : 0.659 12.056 13477 Z= 0.390 Chirality : 0.043 0.211 1536 Planarity : 0.005 0.056 944 Dihedral : 31.404 171.910 2968 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.72 % Allowed : 28.38 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.36), residues: 512 helix: 2.04 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.80 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 72 TYR 0.024 0.002 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.18 ( 9282) covalent geometry : angle 0.65908 / 0.39 (13477) hydrogen bonds : bond 0.05544 / 3.72 ( 559) hydrogen bonds : angle 3.17889 / 2.28 ( 1378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8604 (tp) cc_final: 0.8321 (tt) REVERT: A 125 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: A 128 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8180 (mmm-85) REVERT: B 88 TYR cc_start: 0.8061 (m-80) cc_final: 0.7805 (m-80) REVERT: B 91 LYS cc_start: 0.8667 (mttm) cc_final: 0.8411 (mtmm) REVERT: C 56 GLU cc_start: 0.8223 (tp30) cc_final: 0.7715 (tp30) REVERT: C 57 TYR cc_start: 0.8040 (t80) cc_final: 0.7762 (t80) REVERT: C 64 GLU cc_start: 0.8167 (tp30) cc_final: 0.7882 (tp30) REVERT: C 68 ASN cc_start: 0.8120 (m-40) cc_final: 0.7060 (m-40) REVERT: C 72 ASP cc_start: 0.8332 (m-30) cc_final: 0.7941 (m-30) REVERT: C 99 ARG cc_start: 0.8097 (mpt180) cc_final: 0.7757 (mpt180) REVERT: D 39 TYR cc_start: 0.8360 (t80) cc_final: 0.8061 (t80) REVERT: D 43 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8621 (mmmm) REVERT: D 44 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8528 (tm-30) REVERT: D 54 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8745 (mmmm) REVERT: D 60 ASN cc_start: 0.8650 (t0) cc_final: 0.8442 (t0) REVERT: D 65 ASP cc_start: 0.8075 (t0) cc_final: 0.7792 (t0) REVERT: D 69 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8519 (mtp180) REVERT: F 87 VAL cc_start: 0.9215 (t) cc_final: 0.8804 (t) REVERT: F 88 TYR cc_start: 0.8461 (m-80) cc_final: 0.7925 (m-80) REVERT: F 91 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7976 (mtmt) outliers start: 25 outliers final: 18 residues processed: 229 average time/residue: 0.1196 time to fit residues: 34.1344 Evaluate side-chains 245 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 40 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS C 73 ASN E 108 ASN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.133132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109186 restraints weight = 16757.042| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.97 r_work: 0.3516 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9282 Z= 0.151 Angle : 0.636 11.852 13477 Z= 0.379 Chirality : 0.041 0.208 1536 Planarity : 0.004 0.045 944 Dihedral : 31.338 171.277 2968 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.12 % Allowed : 30.21 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.37), residues: 512 helix: 2.12 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.77 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 72 TYR 0.021 0.002 TYR D 80 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 ( 9282) covalent geometry : angle 0.63636 / 0.38 (13477) hydrogen bonds : bond 0.05039 / 3.38 ( 559) hydrogen bonds : angle 3.06341 / 2.21 ( 1378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8610 (tp) cc_final: 0.8322 (tt) REVERT: A 125 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: A 128 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8187 (mmm-85) REVERT: B 88 TYR cc_start: 0.8041 (m-80) cc_final: 0.7698 (m-80) REVERT: B 91 LYS cc_start: 0.8611 (mttm) cc_final: 0.8340 (mtmm) REVERT: C 56 GLU cc_start: 0.8179 (tp30) cc_final: 0.7630 (tp30) REVERT: C 64 GLU cc_start: 0.8114 (tp30) cc_final: 0.7801 (tp30) REVERT: C 68 ASN cc_start: 0.8042 (m-40) cc_final: 0.6861 (m-40) REVERT: C 72 ASP cc_start: 0.8266 (m-30) cc_final: 0.7849 (m-30) REVERT: C 99 ARG cc_start: 0.8090 (mpt180) cc_final: 0.7754 (mpt180) REVERT: D 39 TYR cc_start: 0.8304 (t80) cc_final: 0.7987 (t80) REVERT: D 43 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8604 (mmmm) REVERT: D 44 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 60 ASN cc_start: 0.8623 (t0) cc_final: 0.8408 (t0) REVERT: D 65 ASP cc_start: 0.8083 (t0) cc_final: 0.7787 (t0) REVERT: D 69 ARG cc_start: 0.8809 (ttm170) cc_final: 0.8505 (mtp180) REVERT: F 71 THR cc_start: 0.8893 (m) cc_final: 0.8499 (p) REVERT: F 87 VAL cc_start: 0.9185 (t) cc_final: 0.8749 (t) REVERT: F 88 TYR cc_start: 0.8442 (m-80) cc_final: 0.7902 (m-80) REVERT: F 91 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7965 (mtmt) outliers start: 18 outliers final: 13 residues processed: 224 average time/residue: 0.1286 time to fit residues: 35.4801 Evaluate side-chains 236 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 0.0020 chunk 16 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 31 HIS E 108 ASN F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.133149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109164 restraints weight = 16727.587| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.98 r_work: 0.3515 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9282 Z= 0.155 Angle : 0.645 13.462 13477 Z= 0.381 Chirality : 0.042 0.260 1536 Planarity : 0.004 0.053 944 Dihedral : 31.330 171.300 2968 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.89 % Allowed : 29.75 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.37), residues: 512 helix: 2.15 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.78 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 72 TYR 0.058 0.003 TYR C 57 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.16 ( 9282) covalent geometry : angle 0.64520 / 0.38 (13477) hydrogen bonds : bond 0.05069 / 3.39 ( 559) hydrogen bonds : angle 3.09671 / 2.23 ( 1378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8604 (tp) cc_final: 0.8325 (tt) REVERT: A 125 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: A 128 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8222 (mmm-85) REVERT: B 88 TYR cc_start: 0.8023 (m-80) cc_final: 0.7813 (m-80) REVERT: B 91 LYS cc_start: 0.8613 (mttm) cc_final: 0.8346 (mtmm) REVERT: C 56 GLU cc_start: 0.8162 (tp30) cc_final: 0.7629 (tp30) REVERT: C 61 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: C 64 GLU cc_start: 0.8101 (tp30) cc_final: 0.7775 (tp30) REVERT: C 68 ASN cc_start: 0.8031 (m-40) cc_final: 0.6831 (m-40) REVERT: C 72 ASP cc_start: 0.8266 (m-30) cc_final: 0.7844 (m-30) REVERT: C 99 ARG cc_start: 0.8105 (mpt180) cc_final: 0.7771 (mpt180) REVERT: D 39 TYR cc_start: 0.8325 (t80) cc_final: 0.8007 (t80) REVERT: D 43 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8596 (mmmm) REVERT: D 44 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8503 (tm-30) REVERT: D 60 ASN cc_start: 0.8621 (t0) cc_final: 0.8409 (t0) REVERT: D 65 ASP cc_start: 0.8087 (t0) cc_final: 0.7792 (t0) REVERT: D 69 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8503 (mtp180) REVERT: F 71 THR cc_start: 0.8881 (m) cc_final: 0.8490 (p) REVERT: F 87 VAL cc_start: 0.9171 (t) cc_final: 0.8740 (t) REVERT: F 88 TYR cc_start: 0.8446 (m-80) cc_final: 0.7887 (m-80) REVERT: F 91 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7954 (mtmt) outliers start: 17 outliers final: 13 residues processed: 225 average time/residue: 0.1339 time to fit residues: 37.1180 Evaluate side-chains 238 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.0010 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS C 73 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108996 restraints weight = 16731.337| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.98 r_work: 0.3514 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 9282 Z= 0.222 Angle : 0.920 59.200 13477 Z= 0.565 Chirality : 0.043 0.426 1536 Planarity : 0.005 0.054 944 Dihedral : 31.326 171.329 2968 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.12 % Allowed : 29.75 % Favored : 66.13 % Cbeta Deviations : 0.20 % 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: 2.05 (0.37), residues: 512 helix: 2.07 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.78 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 72 TYR 0.048 0.003 TYR C 57 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.22 ( 9282) covalent geometry : angle 0.92039 / 0.57 (13477) hydrogen bonds : bond 0.05113 / 3.42 ( 559) hydrogen bonds : angle 3.10107 / 2.23 ( 1378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.91 seconds wall clock time: 38 minutes 51.15 seconds (2331.15 seconds total)