Starting phenix.real_space_refine on Wed Aug 5 04:13:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etv_28600/08_2026/8etv_28600_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etv_28600/08_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_28600/08_2026/8etv_28600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etv_28600/08_2026/8etv_28600.map" model { file = "/net/cci-nas-00/data/ceres_data/8etv_28600/08_2026/8etv_28600_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etv_28600/08_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-2.2rc3-6140/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: 1.72, per 1000 atoms: 0.20 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: 0.47 Conformation dependent library (CDL) restraints added in 298.2 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: 1.06 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: 1.16 Time building geometry restraints manager: 0.64 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: 8.990 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.440 Find NCS groups from input model: 0.070 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.740 ------------------------------------------------------------------------------- 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 : 1.009 14.501 13477 Z= 0.802 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 1.00945 / 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 : 0.143 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: 0.7355 (mp10) REVERT: B 66 ILE cc_start: 0.8802 (mm) cc_final: 0.8580 (tp) REVERT: B 73 THR cc_start: 0.8696 (m) cc_final: 0.8431 (m) REVERT: B 81 VAL cc_start: 0.8703 (t) cc_final: 0.8438 (t) REVERT: B 82 THR cc_start: 0.8609 (t) cc_final: 0.8054 (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: 0.7317 (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: 0.7524 (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: 0.6751 (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: 0.8524 (mtp180) REVERT: E 59 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6672 (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: 0.7526 (tt0) REVERT: E 69 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7783 (ttm110) REVERT: E 92 LEU cc_start: 0.8634 (mt) cc_final: 0.8413 (mt) REVERT: E 96 SER cc_start: 0.8310 (m) cc_final: 0.8064 (m) REVERT: F 26 ILE cc_start: 0.8937 (tp) cc_final: 0.8691 (tt) REVERT: F 88 TYR cc_start: 0.8081 (m-80) cc_final: 0.7819 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1262 time to fit residues: 34.7431 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 : 0.189 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 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 ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3985 r_free = 0.3985 target = 0.127606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103741 restraints weight = 16747.104| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.98 r_work: 0.3423 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1607 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= 0.405 Angle : 0.882 12.096 13477 Z= 0.502 Chirality : 0.055 0.233 1536 Planarity : 0.007 0.066 944 Dihedral : 31.450 174.260 2968 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.89 % Allowed : 17.16 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.34), residues: 512 helix: 0.77 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 42 TYR 0.046 0.004 TYR B 88 PHE 0.012 0.002 PHE D 67 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.41 ( 9282) covalent geometry : angle 0.88186 / 0.50 (13477) hydrogen bonds : bond 0.08296 / 5.61 ( 559) hydrogen bonds : angle 3.71484 / 2.69 ( 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 : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7970 (ttp-110) REVERT: B 27 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8207 (mm-40) REVERT: B 52 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 82 THR cc_start: 0.8716 (t) cc_final: 0.8236 (p) REVERT: B 88 TYR cc_start: 0.8003 (m-80) cc_final: 0.7453 (m-80) REVERT: C 17 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7513 (ptm160) REVERT: C 57 TYR cc_start: 0.8362 (t80) cc_final: 0.7570 (t80) REVERT: C 61 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: C 64 GLU cc_start: 0.8361 (tp30) cc_final: 0.8144 (tp30) REVERT: C 68 ASN cc_start: 0.8375 (m-40) cc_final: 0.7385 (m110) REVERT: C 72 ASP cc_start: 0.8444 (m-30) cc_final: 0.8168 (m-30) REVERT: C 99 ARG cc_start: 0.8194 (mpt180) cc_final: 0.7894 (mpt180) REVERT: D 43 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8718 (mmmm) REVERT: D 44 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 60 ASN cc_start: 0.8725 (t0) cc_final: 0.8505 (t0) REVERT: D 69 ARG cc_start: 0.8874 (ttm170) cc_final: 0.8589 (mtp180) REVERT: E 68 GLN cc_start: 0.8316 (tt0) cc_final: 0.8080 (tt0) REVERT: E 99 TYR cc_start: 0.8328 (t80) cc_final: 0.8084 (t80) REVERT: E 116 ARG cc_start: 0.8239 (mtm110) cc_final: 0.7874 (mtm110) REVERT: E 120 MET cc_start: 0.7679 (mtp) cc_final: 0.7388 (mtm) REVERT: F 88 TYR cc_start: 0.8564 (m-80) cc_final: 0.7901 (m-80) REVERT: F 91 LYS cc_start: 0.8266 (mtmt) cc_final: 0.8038 (mtmt) outliers start: 17 outliers final: 11 residues processed: 242 average time/residue: 0.1313 time to fit residues: 38.7505 Evaluate side-chains 253 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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: 0.2980 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4033 r_free = 0.4033 target = 0.130919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106681 restraints weight = 16446.631| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.96 r_work: 0.3480 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9282 Z= 0.188 Angle : 0.693 11.707 13477 Z= 0.409 Chirality : 0.045 0.228 1536 Planarity : 0.005 0.060 944 Dihedral : 31.477 174.734 2968 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.03 % Allowed : 23.80 % Favored : 71.17 % 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: 1.37 (0.36), residues: 512 helix: 1.57 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.86 (0.47), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 77 TYR 0.024 0.003 TYR B 88 PHE 0.010 0.002 PHE F 61 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.19 ( 9282) covalent geometry : angle 0.69304 / 0.41 (13477) hydrogen bonds : bond 0.06036 / 4.07 ( 559) hydrogen bonds : angle 3.20915 / 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 254 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8069 (mm-40) REVERT: B 82 THR cc_start: 0.8691 (t) cc_final: 0.8246 (p) REVERT: B 91 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8365 (mttm) REVERT: C 17 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7440 (ptm160) REVERT: C 64 GLU cc_start: 0.8286 (tp30) cc_final: 0.8036 (tp30) REVERT: C 68 ASN cc_start: 0.8213 (m-40) cc_final: 0.7128 (m110) REVERT: C 72 ASP cc_start: 0.8337 (m-30) cc_final: 0.7975 (m-30) REVERT: C 99 ARG cc_start: 0.8145 (mpt180) cc_final: 0.7822 (mpt180) REVERT: D 43 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8635 (mmmm) REVERT: D 44 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8470 (tm-30) REVERT: D 60 ASN cc_start: 0.8698 (t0) cc_final: 0.8477 (t0) REVERT: D 65 ASP cc_start: 0.8086 (t0) cc_final: 0.7855 (t0) REVERT: D 69 ARG cc_start: 0.8859 (ttm170) cc_final: 0.8577 (mtp180) REVERT: E 68 GLN cc_start: 0.8219 (tt0) cc_final: 0.7953 (tt0) REVERT: E 120 MET cc_start: 0.7543 (mtp) cc_final: 0.7239 (mtp) REVERT: E 129 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8318 (mmm-85) REVERT: F 88 TYR cc_start: 0.8502 (m-80) cc_final: 0.8228 (m-80) outliers start: 22 outliers final: 16 residues processed: 233 average time/residue: 0.1258 time to fit residues: 36.1843 Evaluate side-chains 247 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 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 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 E residue 124 ILE Chi-restraints excluded: chain F residue 31 LYS 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: 1.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.0010 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4039 r_free = 0.4039 target = 0.131367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107439 restraints weight = 16710.527| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.97 r_work: 0.3488 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9282 Z= 0.180 Angle : 0.673 11.674 13477 Z= 0.395 Chirality : 0.044 0.222 1536 Planarity : 0.005 0.059 944 Dihedral : 31.453 174.229 2968 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.41 % Allowed : 23.11 % Favored : 70.48 % 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: 1.75 (0.37), residues: 512 helix: 1.86 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.77 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 49 TYR 0.026 0.003 TYR D 39 PHE 0.009 0.002 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.18 ( 9282) covalent geometry : angle 0.67258 / 0.40 (13477) hydrogen bonds : bond 0.05678 / 3.81 ( 559) hydrogen bonds : angle 3.15108 / 2.26 ( 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 259 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: B 27 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8124 (mm-40) REVERT: B 55 ARG cc_start: 0.8735 (mtt90) cc_final: 0.8504 (mtt180) REVERT: C 17 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7429 (ptm160) REVERT: C 56 GLU cc_start: 0.8161 (tp30) cc_final: 0.7611 (tp30) REVERT: C 64 GLU cc_start: 0.8241 (tp30) cc_final: 0.7975 (tp30) REVERT: C 68 ASN cc_start: 0.8175 (m-40) cc_final: 0.7012 (m-40) REVERT: C 72 ASP cc_start: 0.8327 (m-30) cc_final: 0.7939 (m-30) REVERT: C 99 ARG cc_start: 0.8128 (mpt180) cc_final: 0.7800 (mpt180) REVERT: D 43 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8644 (mmmm) REVERT: D 44 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8467 (tm-30) REVERT: D 60 ASN cc_start: 0.8673 (t0) cc_final: 0.8442 (t0) REVERT: D 65 ASP cc_start: 0.8078 (t0) cc_final: 0.7807 (t0) REVERT: D 69 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8555 (mtp180) REVERT: E 68 GLN cc_start: 0.8215 (tt0) cc_final: 0.7942 (tt0) REVERT: E 90 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7170 (mpp) REVERT: E 120 MET cc_start: 0.7489 (mtp) cc_final: 0.7200 (mtp) REVERT: E 129 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8361 (mmm-85) REVERT: E 131 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8266 (mtt180) REVERT: F 87 VAL cc_start: 0.9178 (t) cc_final: 0.8739 (t) REVERT: F 88 TYR cc_start: 0.8507 (m-80) cc_final: 0.7939 (m-80) REVERT: F 91 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7946 (mtmt) outliers start: 28 outliers final: 20 residues processed: 234 average time/residue: 0.1358 time to fit residues: 39.1888 Evaluate side-chains 251 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 76 GLN Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 109 LEU 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: 0.5980 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 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 = 0.4048 r_free = 0.4048 target = 0.131739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.107642 restraints weight = 16714.929| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.97 r_work: 0.3493 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2060 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= 0.174 Angle : 0.656 11.925 13477 Z= 0.386 Chirality : 0.043 0.227 1536 Planarity : 0.005 0.056 944 Dihedral : 31.406 173.320 2968 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.64 % Allowed : 23.57 % 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: 2.03 (0.37), residues: 512 helix: 2.05 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.59 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 49 TYR 0.026 0.002 TYR D 39 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 ( 9282) covalent geometry : angle 0.65551 / 0.39 (13477) hydrogen bonds : bond 0.05415 / 3.64 ( 559) hydrogen bonds : angle 3.06906 / 2.20 ( 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: 29 poor density : 231 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: A 128 ARG cc_start: 0.8439 (mtp85) cc_final: 0.8204 (mtm-85) REVERT: B 27 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8121 (mm-40) REVERT: B 55 ARG cc_start: 0.8743 (mtt90) cc_final: 0.8513 (mtt180) REVERT: B 67 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7997 (ttm-80) REVERT: B 91 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8351 (mttm) REVERT: C 17 ARG cc_start: 0.7964 (ptm160) cc_final: 0.7424 (ptm160) REVERT: C 42 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: C 56 GLU cc_start: 0.8199 (tp30) cc_final: 0.7721 (tp30) REVERT: C 57 TYR cc_start: 0.8164 (t80) cc_final: 0.7875 (t80) REVERT: C 64 GLU cc_start: 0.8209 (tp30) cc_final: 0.7860 (tp30) REVERT: C 68 ASN cc_start: 0.8157 (m-40) cc_final: 0.6961 (m-40) REVERT: C 72 ASP cc_start: 0.8332 (m-30) cc_final: 0.7930 (m-30) REVERT: C 99 ARG cc_start: 0.8132 (mpt180) cc_final: 0.7806 (mpt180) REVERT: D 43 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8646 (mmmm) REVERT: D 44 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8466 (tm-30) REVERT: D 60 ASN cc_start: 0.8661 (t0) cc_final: 0.8447 (t0) REVERT: D 65 ASP cc_start: 0.8079 (t0) cc_final: 0.7786 (t0) REVERT: D 69 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8553 (mtp180) REVERT: D 85 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8024 (p) REVERT: E 68 GLN cc_start: 0.8207 (tt0) cc_final: 0.7928 (tt0) REVERT: E 90 MET cc_start: 0.7752 (mpp) cc_final: 0.7546 (mmm) REVERT: E 120 MET cc_start: 0.7487 (mtp) cc_final: 0.7212 (mtp) REVERT: E 129 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8354 (mmm-85) REVERT: F 88 TYR cc_start: 0.8496 (m-80) cc_final: 0.7937 (m-80) REVERT: F 91 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7942 (mtmt) outliers start: 29 outliers final: 21 residues processed: 233 average time/residue: 0.1312 time to fit residues: 37.7740 Evaluate side-chains 253 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU 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 85 THR 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 E residue 124 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: 1.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.130586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106793 restraints weight = 16729.806| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.96 r_work: 0.3477 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9282 Z= 0.208 Angle : 0.674 12.162 13477 Z= 0.395 Chirality : 0.044 0.225 1536 Planarity : 0.005 0.058 944 Dihedral : 31.408 173.028 2968 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 6.64 % Allowed : 25.17 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.37), residues: 512 helix: 1.96 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.61 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 45 TYR 0.027 0.002 TYR D 39 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 0.00371 / 0.21 ( 9282) covalent geometry : angle 0.67412 / 0.40 (13477) hydrogen bonds : bond 0.05855 / 3.92 ( 559) hydrogen bonds : angle 3.18772 / 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 258 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: B 27 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8038 (mm-40) REVERT: B 36 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8367 (mtm-85) REVERT: B 67 ARG cc_start: 0.8341 (ttm170) cc_final: 0.8024 (ttm-80) REVERT: B 91 LYS cc_start: 0.8630 (mtmm) cc_final: 0.8374 (mttm) REVERT: C 17 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7437 (ptm160) REVERT: C 56 GLU cc_start: 0.8248 (tp30) cc_final: 0.7745 (tp30) REVERT: C 64 GLU cc_start: 0.8206 (tp30) cc_final: 0.7844 (tp30) REVERT: C 68 ASN cc_start: 0.8122 (m-40) cc_final: 0.6939 (m-40) REVERT: C 72 ASP cc_start: 0.8336 (m-30) cc_final: 0.7952 (m-30) REVERT: C 99 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7791 (mpt180) REVERT: D 43 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8653 (mmmm) REVERT: D 44 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8473 (tm-30) REVERT: D 60 ASN cc_start: 0.8669 (t0) cc_final: 0.8454 (t0) REVERT: D 65 ASP cc_start: 0.8084 (t0) cc_final: 0.7805 (t0) REVERT: D 69 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8539 (mtp180) REVERT: D 85 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8192 (p) REVERT: E 61 LEU cc_start: 0.8934 (mm) cc_final: 0.8710 (mm) REVERT: E 68 GLN cc_start: 0.8231 (tt0) cc_final: 0.7945 (tt0) REVERT: E 90 MET cc_start: 0.7761 (mpp) cc_final: 0.7545 (mmm) REVERT: E 120 MET cc_start: 0.7537 (mtp) cc_final: 0.7241 (mtp) REVERT: F 87 VAL cc_start: 0.9222 (t) cc_final: 0.8805 (t) REVERT: F 88 TYR cc_start: 0.8508 (m-80) cc_final: 0.7949 (m-80) REVERT: F 91 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7968 (mtmt) outliers start: 29 outliers final: 22 residues processed: 232 average time/residue: 0.1321 time to fit residues: 37.9211 Evaluate side-chains 250 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU 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 85 THR 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 108 ASN Chi-restraints excluded: chain E residue 109 LEU 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: 0.9980 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 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 = 0.4034 r_free = 0.4034 target = 0.130848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.107065 restraints weight = 16849.125| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.97 r_work: 0.3482 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9282 Z= 0.199 Angle : 0.669 11.550 13477 Z= 0.392 Chirality : 0.044 0.227 1536 Planarity : 0.005 0.057 944 Dihedral : 31.391 172.684 2968 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.86 % Allowed : 26.54 % Favored : 66.59 % 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: 1.96 (0.36), residues: 512 helix: 1.99 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.61 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 45 TYR 0.027 0.002 TYR C 57 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 0.00353 / 0.20 ( 9282) covalent geometry : angle 0.66892 / 0.39 (13477) hydrogen bonds : bond 0.05761 / 3.85 ( 559) hydrogen bonds : angle 3.18909 / 2.30 ( 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: 30 poor density : 230 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7283 (mp10) REVERT: A 128 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8183 (mtm-85) REVERT: B 27 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8122 (mm-40) REVERT: B 67 ARG cc_start: 0.8307 (ttm170) cc_final: 0.8001 (ttm-80) REVERT: B 91 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8389 (mttm) REVERT: C 17 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7429 (ptm160) REVERT: C 56 GLU cc_start: 0.8228 (tp30) cc_final: 0.7719 (tp30) REVERT: C 61 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: C 64 GLU cc_start: 0.8186 (tp30) cc_final: 0.7870 (tp30) REVERT: C 68 ASN cc_start: 0.8136 (m-40) cc_final: 0.7029 (m-40) REVERT: C 72 ASP cc_start: 0.8327 (m-30) cc_final: 0.7940 (m-30) REVERT: C 99 ARG cc_start: 0.8118 (mpt180) cc_final: 0.7779 (mpt180) REVERT: D 43 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8656 (mmmm) REVERT: D 44 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8476 (tm-30) REVERT: D 54 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8666 (mmmm) REVERT: D 60 ASN cc_start: 0.8657 (t0) cc_final: 0.8441 (t0) REVERT: D 65 ASP cc_start: 0.8081 (t0) cc_final: 0.7803 (t0) REVERT: D 69 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8533 (mtp180) REVERT: D 85 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8189 (p) REVERT: E 61 LEU cc_start: 0.8943 (mm) cc_final: 0.8708 (mm) REVERT: E 68 GLN cc_start: 0.8233 (tt0) cc_final: 0.7953 (tt0) REVERT: E 90 MET cc_start: 0.7736 (mpp) cc_final: 0.7523 (mmm) REVERT: F 87 VAL cc_start: 0.9219 (t) cc_final: 0.8808 (t) REVERT: F 88 TYR cc_start: 0.8485 (m-80) cc_final: 0.7940 (m-80) REVERT: F 91 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7983 (mtmt) outliers start: 30 outliers final: 22 residues processed: 236 average time/residue: 0.1223 time to fit residues: 35.8528 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 : 0.143 ------------------------------------------------------------------------------- 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 C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU 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 85 THR 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 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: 0.5980 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 0.1980 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.132170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.108166 restraints weight = 16729.539| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.97 r_work: 0.3501 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2253 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= 0.164 Angle : 0.644 13.124 13477 Z= 0.380 Chirality : 0.043 0.227 1536 Planarity : 0.005 0.056 944 Dihedral : 31.342 172.120 2968 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.49 % Allowed : 28.60 % 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: 2.11 (0.37), residues: 512 helix: 2.08 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.53 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 45 TYR 0.024 0.002 TYR D 39 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 0.00281 / 0.16 ( 9282) covalent geometry : angle 0.64366 / 0.38 (13477) hydrogen bonds : bond 0.05320 / 3.55 ( 559) hydrogen bonds : angle 3.09452 / 2.23 ( 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 253 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: B 36 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8389 (mtm-85) REVERT: B 87 VAL cc_start: 0.8918 (t) cc_final: 0.8459 (p) REVERT: B 91 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8266 (mttm) REVERT: C 56 GLU cc_start: 0.8216 (tp30) cc_final: 0.7728 (tp30) REVERT: C 64 GLU cc_start: 0.8136 (tp30) cc_final: 0.7865 (tp30) REVERT: C 68 ASN cc_start: 0.8100 (m-40) cc_final: 0.6980 (m-40) REVERT: C 72 ASP cc_start: 0.8297 (m-30) cc_final: 0.7880 (m-30) REVERT: C 99 ARG cc_start: 0.8126 (mpt180) cc_final: 0.7790 (mpt180) REVERT: D 43 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8635 (mmmm) REVERT: D 44 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 54 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8751 (mmmm) REVERT: D 60 ASN cc_start: 0.8635 (t0) cc_final: 0.8421 (t0) REVERT: D 65 ASP cc_start: 0.8085 (t0) cc_final: 0.7795 (t0) REVERT: D 69 ARG cc_start: 0.8825 (ttm170) cc_final: 0.8531 (mtp180) REVERT: D 85 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8136 (p) REVERT: E 68 GLN cc_start: 0.8204 (tt0) cc_final: 0.7915 (tt0) REVERT: E 90 MET cc_start: 0.7735 (mpp) cc_final: 0.7507 (mmm) REVERT: F 87 VAL cc_start: 0.9189 (t) cc_final: 0.8781 (t) REVERT: F 88 TYR cc_start: 0.8451 (m-80) cc_final: 0.7906 (m-80) REVERT: F 91 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7960 (mtmt) outliers start: 24 outliers final: 17 residues processed: 232 average time/residue: 0.1209 time to fit residues: 34.7642 Evaluate side-chains 248 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU 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 85 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 0.0870 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 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 = 0.4062 r_free = 0.4062 target = 0.132623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108615 restraints weight = 16792.518| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.98 r_work: 0.3506 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9282 Z= 0.161 Angle : 0.645 12.650 13477 Z= 0.378 Chirality : 0.042 0.225 1536 Planarity : 0.004 0.048 944 Dihedral : 31.271 171.894 2968 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.58 % Allowed : 29.29 % Favored : 66.13 % 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: 2.19 (0.37), residues: 512 helix: 2.12 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 55 TYR 0.025 0.002 TYR C 57 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 0.00275 / 0.16 ( 9282) covalent geometry : angle 0.64487 / 0.38 (13477) hydrogen bonds : bond 0.05210 / 3.48 ( 559) hydrogen bonds : angle 3.07407 / 2.22 ( 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 248 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: B 87 VAL cc_start: 0.8903 (t) cc_final: 0.8462 (p) REVERT: B 91 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8301 (mttm) REVERT: C 17 ARG cc_start: 0.8527 (mtm180) cc_final: 0.8321 (mtm180) REVERT: C 56 GLU cc_start: 0.8207 (tp30) cc_final: 0.7700 (tp30) REVERT: C 64 GLU cc_start: 0.8117 (tp30) cc_final: 0.7784 (tp30) REVERT: C 68 ASN cc_start: 0.8070 (m-40) cc_final: 0.6869 (m-40) REVERT: C 72 ASP cc_start: 0.8302 (m-30) cc_final: 0.7875 (m-30) REVERT: C 99 ARG cc_start: 0.8138 (mpt180) cc_final: 0.7798 (mpt180) REVERT: D 43 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8634 (mmmm) REVERT: D 44 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8494 (tm-30) REVERT: D 60 ASN cc_start: 0.8605 (t0) cc_final: 0.8390 (t0) REVERT: D 65 ASP cc_start: 0.8099 (t0) cc_final: 0.7801 (t0) REVERT: D 69 ARG cc_start: 0.8814 (ttm170) cc_final: 0.8526 (mtp180) REVERT: D 85 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8125 (p) REVERT: E 90 MET cc_start: 0.7761 (mpp) cc_final: 0.7514 (mmm) REVERT: F 71 THR cc_start: 0.8871 (m) cc_final: 0.8493 (p) REVERT: F 87 VAL cc_start: 0.9166 (t) cc_final: 0.8756 (t) REVERT: F 88 TYR cc_start: 0.8456 (m-80) cc_final: 0.7893 (m-80) REVERT: F 91 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7942 (mtmt) outliers start: 20 outliers final: 16 residues processed: 231 average time/residue: 0.1143 time to fit residues: 32.5975 Evaluate side-chains 245 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU 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 85 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 108 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.0020 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.133342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109397 restraints weight = 16740.191| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.97 r_work: 0.3518 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2377 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= 0.149 Angle : 0.636 12.542 13477 Z= 0.373 Chirality : 0.042 0.225 1536 Planarity : 0.005 0.056 944 Dihedral : 31.232 171.736 2968 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.12 % Allowed : 30.43 % Favored : 65.45 % 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: 2.25 (0.37), residues: 512 helix: 2.15 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.54 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 55 TYR 0.026 0.002 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 0.00254 / 0.15 ( 9282) covalent geometry : angle 0.63592 / 0.37 (13477) hydrogen bonds : bond 0.05083 / 3.38 ( 559) hydrogen bonds : angle 3.03415 / 2.19 ( 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 246 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: B 87 VAL cc_start: 0.8869 (t) cc_final: 0.8550 (p) REVERT: B 91 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8287 (mtmm) REVERT: C 17 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8265 (mtm180) REVERT: C 56 GLU cc_start: 0.8170 (tp30) cc_final: 0.7687 (tp30) REVERT: C 57 TYR cc_start: 0.8038 (t80) cc_final: 0.6994 (t80) REVERT: C 61 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: C 68 ASN cc_start: 0.8053 (m-40) cc_final: 0.7525 (m-40) REVERT: C 72 ASP cc_start: 0.8277 (m-30) cc_final: 0.7852 (m-30) REVERT: C 99 ARG cc_start: 0.8124 (mpt180) cc_final: 0.7791 (mpt180) REVERT: D 43 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8611 (mmmm) REVERT: D 44 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8493 (tm-30) REVERT: D 60 ASN cc_start: 0.8598 (t0) cc_final: 0.8381 (t0) REVERT: D 65 ASP cc_start: 0.8077 (t0) cc_final: 0.7778 (t0) REVERT: D 69 ARG cc_start: 0.8803 (ttm170) cc_final: 0.8515 (mtp180) REVERT: D 80 TYR cc_start: 0.7273 (m-10) cc_final: 0.6991 (m-10) REVERT: D 85 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8105 (p) REVERT: E 90 MET cc_start: 0.7771 (mpp) cc_final: 0.7510 (mmm) REVERT: F 71 THR cc_start: 0.8863 (m) cc_final: 0.8498 (p) REVERT: F 87 VAL cc_start: 0.9161 (t) cc_final: 0.8746 (t) REVERT: F 88 TYR cc_start: 0.8428 (m-80) cc_final: 0.7879 (m-80) REVERT: F 91 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7934 (mtmt) outliers start: 18 outliers final: 15 residues processed: 231 average time/residue: 0.1031 time to fit residues: 29.6038 Evaluate side-chains 246 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU 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 85 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 108 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 72 TYR 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: 0.8980 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109028 restraints weight = 16760.687| |-----------------------------------------------------------------------------| r_work (start): 0.3687 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: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 9282 Z= 0.212 Angle : 0.911 59.167 13477 Z= 0.552 Chirality : 0.043 0.229 1536 Planarity : 0.005 0.062 944 Dihedral : 31.220 171.803 2968 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.58 % Allowed : 30.43 % Favored : 64.99 % 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: 2.16 (0.37), residues: 512 helix: 2.08 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -0.55 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 55 TYR 0.024 0.002 TYR D 39 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 0.00361 / 0.21 ( 9282) covalent geometry : angle 0.91136 / 0.55 (13477) hydrogen bonds : bond 0.05167 / 3.43 ( 559) hydrogen bonds : angle 3.04284 / 2.20 ( 1378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.12 seconds wall clock time: 33 minutes 45.63 seconds (2025.63 seconds total)