Starting phenix.real_space_refine on Sat Mar 16 12:33:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/03_2024/7xpx_33385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/03_2024/7xpx_33385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/03_2024/7xpx_33385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/03_2024/7xpx_33385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/03_2024/7xpx_33385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xpx_33385/03_2024/7xpx_33385_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1341 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 20 5.16 5 C 7508 2.51 5 N 2521 2.21 5 O 3071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13408 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 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: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2970 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1365 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1364 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 168, 1364 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 bond proxies already assigned to first conformer: 1388 Time building chain proxies: 7.79, per 1000 atoms: 0.58 Number of scatterers: 13408 At special positions: 0 Unit cell: (94, 120, 121, 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 20 16.00 P 288 15.00 O 3071 8.00 N 2521 7.00 C 7508 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 - 3.50 Amino acid : False - 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: 7.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 3 sheets defined 54.8% alpha, 4.2% beta 137 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.674A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.265A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.798A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.612A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.289A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'K' and resid 200 through 209 removed outlier: 3.720A pdb=" N ARG K 205 " --> pdb=" O GLU K 201 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU K 209 " --> pdb=" O ARG K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 264 removed outlier: 3.982A pdb=" N LYS K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 346 removed outlier: 3.577A pdb=" N GLU K 345 " --> pdb=" O LYS K 341 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA K 346 " --> pdb=" O ALA K 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 341 through 346' Processing sheet with id= A, first strand: chain 'K' and resid 218 through 223 Processing sheet with id= B, first strand: chain 'K' and resid 248 through 250 Processing sheet with id= C, first strand: chain 'K' and resid 305 through 312 removed outlier: 4.525A pdb=" N LEU K 318 " --> pdb=" O TYR K 245 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA K 322 " --> pdb=" O PHE K 241 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE K 241 " --> pdb=" O ALA K 322 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3023 1.34 - 1.46: 4248 1.46 - 1.58: 6355 1.58 - 1.70: 576 1.70 - 1.82: 35 Bond restraints: 14237 Sorted by residual: bond pdb=" C2 SAM K 401 " pdb=" N3 SAM K 401 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" C8 SAM K 401 " pdb=" N7 SAM K 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" CB ECX B 20 " pdb=" SC ECX B 20 " ideal model delta sigma weight residual 1.819 1.767 0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C2 SAM K 401 " pdb=" N1 SAM K 401 " ideal model delta sigma weight residual 1.329 1.380 -0.051 2.00e-02 2.50e+03 6.51e+00 bond pdb=" CD ECX B 20 " pdb=" SC ECX B 20 " ideal model delta sigma weight residual 1.817 1.770 0.047 2.00e-02 2.50e+03 5.51e+00 ... (remaining 14232 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.61: 1409 105.61 - 112.71: 7942 112.71 - 119.81: 4840 119.81 - 126.91: 5509 126.91 - 134.01: 757 Bond angle restraints: 20457 Sorted by residual: angle pdb=" C LYS D 28 " pdb=" CA LYS D 28 " pdb=" CB LYS D 28 " ideal model delta sigma weight residual 116.54 111.52 5.02 1.15e+00 7.56e-01 1.91e+01 angle pdb=" N LYS K 195 " pdb=" CA LYS K 195 " pdb=" C LYS K 195 " ideal model delta sigma weight residual 111.81 107.04 4.77 1.44e+00 4.82e-01 1.10e+01 angle pdb=" CB MET K 272 " pdb=" CG MET K 272 " pdb=" SD MET K 272 " ideal model delta sigma weight residual 112.70 103.62 9.08 3.00e+00 1.11e-01 9.15e+00 angle pdb=" O SAM K 401 " pdb=" C SAM K 401 " pdb=" OXT SAM K 401 " ideal model delta sigma weight residual 126.77 118.08 8.69 3.00e+00 1.11e-01 8.39e+00 angle pdb=" CA LYS D 28 " pdb=" C LYS D 28 " pdb=" N THR D 29 " ideal model delta sigma weight residual 119.52 117.25 2.27 7.90e-01 1.60e+00 8.27e+00 ... (remaining 20452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 6410 35.48 - 70.96: 1429 70.96 - 106.44: 12 106.44 - 141.92: 2 141.92 - 177.40: 3 Dihedral angle restraints: 7856 sinusoidal: 5144 harmonic: 2712 Sorted by residual: dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 42.60 177.40 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I 54 " pdb=" C3' DT I 54 " pdb=" O3' DT I 54 " pdb=" P DC I 55 " ideal model delta sinusoidal sigma weight residual -140.00 36.82 -176.82 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 44.40 175.60 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1725 0.037 - 0.073: 476 0.073 - 0.110: 83 0.110 - 0.147: 25 0.147 - 0.183: 4 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA GLU D 90 " pdb=" N GLU D 90 " pdb=" C GLU D 90 " pdb=" CB GLU D 90 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" C2' SAM K 401 " pdb=" C1' SAM K 401 " pdb=" C3' SAM K 401 " pdb=" O2' SAM K 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" C1' SAM K 401 " pdb=" C2' SAM K 401 " pdb=" N9 SAM K 401 " pdb=" O4' SAM K 401 " both_signs ideal model delta sigma weight residual False 2.30 2.47 -0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 2310 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 55 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ARG B 55 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG B 55 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY B 56 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.027 2.00e-02 2.50e+03 1.19e-02 3.88e+00 pdb=" N9 DA I 47 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL K 315 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO K 316 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO K 316 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 316 " -0.024 5.00e-02 4.00e+02 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 929 2.73 - 3.27: 12442 3.27 - 3.81: 27135 3.81 - 4.36: 32011 4.36 - 4.90: 45836 Nonbonded interactions: 118353 Sorted by model distance: nonbonded pdb=" O LYS C 15 " pdb=" OG SER C 19 " model vdw 2.185 2.440 nonbonded pdb=" O GLU K 208 " pdb=" OG SER K 212 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.227 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.268 2.440 nonbonded pdb=" OE2 GLU D 68 " pdb=" NH2 ARG H 76 " model vdw 2.270 2.520 ... (remaining 118348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 27 through 121) selection = (chain 'H' and resid 27 through 121) } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 44.470 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.004 0.058 14237 Z= 0.216 Angle : 0.612 9.076 20457 Z= 0.359 Chirality : 0.036 0.183 2313 Planarity : 0.005 0.052 1588 Dihedral : 27.533 177.402 6108 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 913 helix: 1.35 (0.21), residues: 572 sheet: -0.78 (0.81), residues: 38 loop : -0.77 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 349 HIS 0.007 0.001 HIS B 75 PHE 0.013 0.002 PHE G 25 TYR 0.019 0.002 TYR K 262 ARG 0.014 0.001 ARG K 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 95 LYS cc_start: 0.7621 (tttm) cc_final: 0.7349 (ttmt) REVERT: D 56 MET cc_start: 0.8281 (tpp) cc_final: 0.8077 (tpp) REVERT: G 75 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8093 (mttm) REVERT: K 195 LYS cc_start: 0.7410 (tmmt) cc_final: 0.7204 (tttt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3548 time to fit residues: 55.0850 Evaluate side-chains 114 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14237 Z= 0.318 Angle : 0.598 6.935 20457 Z= 0.351 Chirality : 0.037 0.162 2313 Planarity : 0.005 0.045 1588 Dihedral : 30.709 177.579 4244 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.02 % Allowed : 5.37 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 913 helix: 1.55 (0.21), residues: 569 sheet: -1.12 (0.79), residues: 40 loop : -0.68 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 349 HIS 0.021 0.001 HIS C 31 PHE 0.010 0.002 PHE E 78 TYR 0.018 0.002 TYR K 277 ARG 0.008 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7488 (tm-30) REVERT: C 95 LYS cc_start: 0.7647 (tttm) cc_final: 0.7373 (ttmt) REVERT: D 56 MET cc_start: 0.8308 (tpp) cc_final: 0.8062 (tpp) REVERT: G 73 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8223 (t0) REVERT: G 75 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8110 (mttm) outliers start: 8 outliers final: 4 residues processed: 118 average time/residue: 0.3467 time to fit residues: 54.3991 Evaluate side-chains 120 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 204 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN D 81 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14237 Z= 0.366 Angle : 0.587 6.016 20457 Z= 0.347 Chirality : 0.037 0.140 2313 Planarity : 0.004 0.041 1588 Dihedral : 30.437 177.727 4244 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.90 % Allowed : 8.44 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 913 helix: 1.43 (0.21), residues: 569 sheet: -0.77 (0.83), residues: 38 loop : -0.65 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.014 0.001 HIS C 31 PHE 0.010 0.002 PHE G 25 TYR 0.013 0.002 TYR K 262 ARG 0.005 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 1.045 Fit side-chains REVERT: C 95 LYS cc_start: 0.7610 (tttm) cc_final: 0.7332 (ttmt) REVERT: D 56 MET cc_start: 0.8268 (tpp) cc_final: 0.8027 (tpp) REVERT: G 73 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8197 (t0) REVERT: G 75 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8149 (mttm) REVERT: H 96 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7423 (mtt-85) outliers start: 7 outliers final: 5 residues processed: 124 average time/residue: 0.3573 time to fit residues: 58.8121 Evaluate side-chains 129 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 204 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.0770 chunk 99 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14237 Z= 0.323 Angle : 0.563 6.534 20457 Z= 0.335 Chirality : 0.036 0.138 2313 Planarity : 0.004 0.039 1588 Dihedral : 30.327 179.251 4244 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.92 % Allowed : 8.57 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 913 helix: 1.46 (0.21), residues: 572 sheet: -0.79 (0.84), residues: 38 loop : -0.62 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.004 0.001 HIS C 31 PHE 0.009 0.002 PHE G 25 TYR 0.012 0.001 TYR K 262 ARG 0.005 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.968 Fit side-chains REVERT: C 95 LYS cc_start: 0.7630 (tttm) cc_final: 0.7329 (ttmt) REVERT: F 90 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8286 (mt) REVERT: G 73 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8206 (t0) REVERT: G 75 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8168 (mttp) REVERT: H 96 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7480 (mtt-85) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.3495 time to fit residues: 61.1844 Evaluate side-chains 138 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS D 81 ASN D 92 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 310 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14237 Z= 0.215 Angle : 0.528 6.944 20457 Z= 0.317 Chirality : 0.034 0.138 2313 Planarity : 0.004 0.039 1588 Dihedral : 30.077 179.391 4244 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.28 % Allowed : 11.00 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.27), residues: 913 helix: 1.76 (0.21), residues: 572 sheet: -0.65 (0.87), residues: 38 loop : -0.56 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE K 275 TYR 0.012 0.001 TYR K 262 ARG 0.005 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7638 (tttm) cc_final: 0.7326 (ttmt) REVERT: F 90 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8310 (mt) REVERT: G 73 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8246 (t0) REVERT: H 96 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.7415 (mtt-85) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 0.3579 time to fit residues: 59.8472 Evaluate side-chains 130 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 204 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 14237 Z= 0.407 Angle : 0.580 6.881 20457 Z= 0.341 Chirality : 0.038 0.141 2313 Planarity : 0.004 0.039 1588 Dihedral : 30.266 178.755 4244 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.92 % Allowed : 11.38 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.27), residues: 913 helix: 1.40 (0.21), residues: 572 sheet: -0.84 (0.85), residues: 38 loop : -0.56 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.002 PHE A 78 TYR 0.012 0.001 TYR F 51 ARG 0.007 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.008 Fit side-chains REVERT: C 95 LYS cc_start: 0.7646 (tttm) cc_final: 0.7360 (ttmt) REVERT: D 98 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8331 (mm) REVERT: F 90 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8334 (mt) REVERT: G 73 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8234 (t0) REVERT: G 75 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8221 (mttm) REVERT: H 96 ARG cc_start: 0.7830 (mtt-85) cc_final: 0.7546 (mtt-85) outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 0.3371 time to fit residues: 60.9652 Evaluate side-chains 143 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14237 Z= 0.187 Angle : 0.533 7.496 20457 Z= 0.320 Chirality : 0.034 0.142 2313 Planarity : 0.004 0.038 1588 Dihedral : 30.189 179.484 4244 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.92 % Allowed : 11.89 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 913 helix: 1.64 (0.21), residues: 573 sheet: -0.66 (0.86), residues: 38 loop : -0.50 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 349 HIS 0.002 0.001 HIS K 347 PHE 0.008 0.001 PHE K 275 TYR 0.013 0.001 TYR F 51 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.027 Fit side-chains REVERT: C 95 LYS cc_start: 0.7605 (tttm) cc_final: 0.7314 (ttmt) REVERT: F 90 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8241 (mt) REVERT: G 73 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8212 (t0) REVERT: G 75 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8143 (mttp) REVERT: H 96 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7489 (mtt-85) outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 0.3329 time to fit residues: 60.1527 Evaluate side-chains 141 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14237 Z= 0.228 Angle : 0.534 7.210 20457 Z= 0.319 Chirality : 0.034 0.137 2313 Planarity : 0.004 0.039 1588 Dihedral : 30.091 179.559 4244 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.79 % Allowed : 12.15 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.28), residues: 913 helix: 1.78 (0.21), residues: 573 sheet: -0.66 (0.85), residues: 38 loop : -0.48 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE K 275 TYR 0.011 0.001 TYR G 57 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.980 Fit side-chains REVERT: C 95 LYS cc_start: 0.7665 (tttm) cc_final: 0.7355 (ttmt) REVERT: F 90 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8294 (mt) REVERT: G 73 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8253 (t0) REVERT: H 96 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.7445 (mtt-85) outliers start: 13 outliers final: 11 residues processed: 131 average time/residue: 0.3310 time to fit residues: 58.3529 Evaluate side-chains 137 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14237 Z= 0.367 Angle : 0.568 7.769 20457 Z= 0.335 Chirality : 0.036 0.136 2313 Planarity : 0.004 0.038 1588 Dihedral : 30.201 178.590 4244 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.17 % Allowed : 11.89 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 913 helix: 1.51 (0.21), residues: 573 sheet: -0.59 (0.86), residues: 38 loop : -0.50 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.002 PHE A 78 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7640 (tttm) cc_final: 0.7334 (ttmt) REVERT: F 90 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8260 (mt) REVERT: G 73 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8245 (t0) REVERT: G 75 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8219 (mttm) REVERT: H 96 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.7559 (mtt-85) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.3583 time to fit residues: 66.7953 Evaluate side-chains 149 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14237 Z= 0.315 Angle : 0.558 8.330 20457 Z= 0.330 Chirality : 0.035 0.138 2313 Planarity : 0.004 0.038 1588 Dihedral : 30.188 178.809 4244 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 2.05 % Allowed : 12.28 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.27), residues: 913 helix: 1.50 (0.21), residues: 572 sheet: -0.51 (0.87), residues: 38 loop : -0.50 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE K 275 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7671 (tttm) cc_final: 0.7373 (ttmt) REVERT: F 90 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8272 (mt) REVERT: G 73 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8235 (t0) REVERT: G 75 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8217 (mttm) REVERT: H 96 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7539 (mtt-85) outliers start: 15 outliers final: 12 residues processed: 141 average time/residue: 0.3510 time to fit residues: 65.6500 Evaluate side-chains 147 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.214776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.125741 restraints weight = 13941.325| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.03 r_work: 0.2945 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14237 Z= 0.167 Angle : 0.524 8.396 20457 Z= 0.312 Chirality : 0.032 0.138 2313 Planarity : 0.004 0.040 1588 Dihedral : 29.912 179.881 4244 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.41 % Favored : 97.48 % Rotamer: Outliers : 1.79 % Allowed : 12.53 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.28), residues: 913 helix: 1.98 (0.22), residues: 574 sheet: -0.50 (0.87), residues: 38 loop : -0.37 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 349 HIS 0.002 0.000 HIS G 82 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR G 57 ARG 0.007 0.000 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2482.15 seconds wall clock time: 45 minutes 31.21 seconds (2731.21 seconds total)