Starting phenix.real_space_refine on Mon Jun 24 19:20:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/06_2024/8wxe_37904_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/06_2024/8wxe_37904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/06_2024/8wxe_37904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/06_2024/8wxe_37904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/06_2024/8wxe_37904_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wxe_37904/06_2024/8wxe_37904_updated.pdb" } resolution = 4.0 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= -0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 2865 2.51 5 N 692 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 124": "OE1" <-> "OE2" Residue "f GLU 86": "OE1" <-> "OE2" Residue "f GLU 89": "OE1" <-> "OE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 257": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4388 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 853 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain breaks: 2 Chain: "f" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 2 Chain: "g" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 821 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 2 Chain: "m" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.75 Number of scatterers: 4388 At special positions: 0 Unit cell: (94.569, 82.612, 98.917, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 794 8.00 N 692 7.00 C 2865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 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: 1.86 Conformation dependent library (CDL) restraints added in 791.9 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 7 sheets defined 40.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'a' and resid 28 through 53 removed outlier: 4.323A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP a 36 " --> pdb=" O CYS a 32 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE a 38 " --> pdb=" O LEU a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 53 Processing helix chain 'd' and resid 101 through 125 removed outlier: 3.562A pdb=" N THR d 110 " --> pdb=" O GLY d 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 151 removed outlier: 4.382A pdb=" N ILE e 133 " --> pdb=" O SER e 129 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL e 134 " --> pdb=" O VAL e 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE e 135 " --> pdb=" O ALA e 131 " (cutoff:3.500A) Processing helix chain 'f' and resid 129 through 152 Processing helix chain 'g' and resid 112 through 139 removed outlier: 4.749A pdb=" N GLY g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 259 through 288 removed outlier: 3.667A pdb=" N PHE m 288 " --> pdb=" O THR m 284 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 287 removed outlier: 3.891A pdb=" N TYR n 264 " --> pdb=" O THR n 260 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET n 265 " --> pdb=" O SER n 261 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL n 275 " --> pdb=" O LEU n 271 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR n 276 " --> pdb=" O LYS n 272 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS n 283 " --> pdb=" O ILE n 279 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'd' and resid 84 through 89 removed outlier: 3.512A pdb=" N VAL d 86 " --> pdb=" O TYR d 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR d 71 " --> pdb=" O VAL d 86 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL d 88 " --> pdb=" O GLY d 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY d 69 " --> pdb=" O VAL d 88 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'd' and resid 32 through 36 removed outlier: 3.864A pdb=" N VAL d 33 " --> pdb=" O GLY d 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY d 61 " --> pdb=" O VAL d 33 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL d 35 " --> pdb=" O ASP d 59 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP d 59 " --> pdb=" O VAL d 35 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'e' and resid 37 through 40 removed outlier: 4.132A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'e' and resid 58 through 61 removed outlier: 3.855A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'f' and resid 45 through 47 removed outlier: 3.536A pdb=" N LEU f 82 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'g' and resid 31 through 34 removed outlier: 4.439A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'g' and resid 55 through 57 removed outlier: 3.814A pdb=" N TRP g 55 " --> pdb=" O GLY g 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY g 63 " --> pdb=" O TRP g 55 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 193 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 2.01 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: 1333 1.34 - 1.47: 1083 1.47 - 1.59: 2000 1.59 - 1.71: 1 1.71 - 1.83: 51 Bond restraints: 4468 Sorted by residual: bond pdb=" CB PRO g 96 " pdb=" CG PRO g 96 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.72e+00 bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.10e+00 bond pdb=" N PRO g 96 " pdb=" CA PRO g 96 " ideal model delta sigma weight residual 1.469 1.450 0.018 1.28e-02 6.10e+03 2.05e+00 bond pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" C3 CLR g 201 " pdb=" O1 CLR g 201 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 4463 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.94: 57 104.94 - 112.21: 2286 112.21 - 119.47: 1402 119.47 - 126.74: 2266 126.74 - 134.00: 40 Bond angle restraints: 6051 Sorted by residual: angle pdb=" CA PRO g 96 " pdb=" N PRO g 96 " pdb=" CD PRO g 96 " ideal model delta sigma weight residual 112.00 98.30 13.70 1.40e+00 5.10e-01 9.58e+01 angle pdb=" CA GLU f 106 " pdb=" CB GLU f 106 " pdb=" CG GLU f 106 " ideal model delta sigma weight residual 114.10 123.42 -9.32 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CB MET f 123 " pdb=" CG MET f 123 " pdb=" SD MET f 123 " ideal model delta sigma weight residual 112.70 124.29 -11.59 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N PRO g 96 " pdb=" CD PRO g 96 " pdb=" CG PRO g 96 " ideal model delta sigma weight residual 103.20 97.67 5.53 1.50e+00 4.44e-01 1.36e+01 angle pdb=" N PRO g 96 " pdb=" CA PRO g 96 " pdb=" CB PRO g 96 " ideal model delta sigma weight residual 103.25 99.87 3.38 1.05e+00 9.07e-01 1.04e+01 ... (remaining 6046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2228 17.86 - 35.72: 372 35.72 - 53.58: 94 53.58 - 71.44: 20 71.44 - 89.30: 4 Dihedral angle restraints: 2718 sinusoidal: 1122 harmonic: 1596 Sorted by residual: dihedral pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " pdb=" SG CYS b 32 " pdb=" CB CYS b 32 " ideal model delta sinusoidal sigma weight residual -86.00 -158.21 72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -147.58 61.58 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.05e+01 ... (remaining 2715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 472 0.034 - 0.068: 170 0.068 - 0.102: 53 0.102 - 0.136: 21 0.136 - 0.170: 5 Chirality restraints: 721 Sorted by residual: chirality pdb=" CA PRO f 105 " pdb=" N PRO f 105 " pdb=" C PRO f 105 " pdb=" CB PRO f 105 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C20 CLR g 201 " pdb=" C17 CLR g 201 " pdb=" C21 CLR g 201 " pdb=" C22 CLR g 201 " both_signs ideal model delta sigma weight residual False 2.59 2.43 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASN g 28 " pdb=" N ASN g 28 " pdb=" C ASN g 28 " pdb=" CB ASN g 28 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 718 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS g 95 " 0.119 5.00e-02 4.00e+02 1.68e-01 4.53e+01 pdb=" N PRO g 96 " -0.290 5.00e-02 4.00e+02 pdb=" CA PRO g 96 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO g 96 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE d 24 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO d 25 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO d 25 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO d 25 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU f 86 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" CD GLU f 86 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU f 86 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU f 86 " -0.013 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 226 2.72 - 3.27: 4476 3.27 - 3.81: 7052 3.81 - 4.36: 7355 4.36 - 4.90: 12734 Nonbonded interactions: 31843 Sorted by model distance: nonbonded pdb=" O SER f 41 " pdb=" OG1 THR f 44 " model vdw 2.178 2.440 nonbonded pdb=" NZ LYS f 104 " pdb=" OE1 GLU f 106 " model vdw 2.199 2.520 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.216 2.440 nonbonded pdb=" N GLU e 124 " pdb=" OE1 GLU e 124 " model vdw 2.272 2.520 nonbonded pdb=" OG SER g 125 " pdb=" NZ LYS n 272 " model vdw 2.321 2.520 ... (remaining 31838 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' selection = chain 'b' } ncs_group { reference = (chain 'e' and (resid 33 through 49 or resid 58 through 65 or resid 75 through 1 \ 53)) selection = (chain 'f' and (resid 33 through 65 or resid 75 through 101 or resid 109 through \ 153)) } 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 group one per residue 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.810 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.210 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 0.130 4468 Z= 0.236 Angle : 0.862 13.704 6051 Z= 0.451 Chirality : 0.043 0.170 721 Planarity : 0.008 0.168 728 Dihedral : 18.180 89.302 1663 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.04 % Allowed : 40.73 % Favored : 57.23 % 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: -0.75 (0.35), residues: 520 helix: 1.55 (0.33), residues: 217 sheet: -1.07 (0.61), residues: 71 loop : -2.43 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 59 HIS 0.005 0.001 HIS g 29 PHE 0.009 0.001 PHE f 110 TYR 0.023 0.001 TYR f 36 ARG 0.007 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 52 ARG cc_start: 0.6571 (ttt180) cc_final: 0.6177 (ttt180) REVERT: d 63 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8450 (mtp85) REVERT: d 92 MET cc_start: 0.8431 (mtp) cc_final: 0.7769 (mmt) REVERT: d 97 VAL cc_start: 0.8955 (t) cc_final: 0.8619 (p) REVERT: d 109 VAL cc_start: 0.8934 (m) cc_final: 0.8674 (p) REVERT: e 92 GLN cc_start: 0.8518 (tt0) cc_final: 0.8028 (tt0) REVERT: e 95 TYR cc_start: 0.6958 (m-80) cc_final: 0.6366 (m-10) REVERT: e 145 LEU cc_start: 0.8539 (mm) cc_final: 0.8173 (tt) REVERT: e 147 LEU cc_start: 0.8127 (tt) cc_final: 0.7907 (mm) REVERT: f 97 VAL cc_start: 0.8610 (m) cc_final: 0.8233 (p) REVERT: f 101 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7068 (mpt180) REVERT: f 121 ASN cc_start: 0.9297 (t0) cc_final: 0.8889 (t0) REVERT: f 125 MET cc_start: 0.7019 (pmm) cc_final: 0.6524 (pmm) REVERT: g 34 TYR cc_start: 0.8520 (t80) cc_final: 0.8285 (t80) REVERT: g 39 ASP cc_start: 0.7355 (m-30) cc_final: 0.6303 (m-30) REVERT: g 73 ASN cc_start: 0.9503 (t0) cc_final: 0.9215 (t0) REVERT: g 103 MET cc_start: 0.7179 (mmp) cc_final: 0.6798 (mmp) REVERT: g 119 LEU cc_start: 0.9204 (tp) cc_final: 0.8856 (tp) REVERT: n 259 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7496 (t0) outliers start: 10 outliers final: 5 residues processed: 221 average time/residue: 0.1566 time to fit residues: 42.9831 Evaluate side-chains 164 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain n residue 259 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 89 HIS e 92 GLN ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4468 Z= 0.234 Angle : 0.746 8.690 6051 Z= 0.370 Chirality : 0.042 0.148 721 Planarity : 0.005 0.088 728 Dihedral : 7.570 57.281 662 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.15 % Allowed : 36.46 % Favored : 55.40 % 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: -0.24 (0.35), residues: 520 helix: 2.22 (0.32), residues: 215 sheet: -0.87 (0.64), residues: 68 loop : -2.34 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP e 59 HIS 0.003 0.001 HIS g 29 PHE 0.020 0.002 PHE g 127 TYR 0.015 0.001 TYR f 149 ARG 0.005 0.001 ARG n 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 52 ARG cc_start: 0.6652 (ttt180) cc_final: 0.6273 (ttt180) REVERT: b 34 LEU cc_start: 0.7974 (tt) cc_final: 0.7252 (mm) REVERT: d 63 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8122 (mtp-110) REVERT: d 72 ARG cc_start: 0.7341 (tpt-90) cc_final: 0.6735 (tpt-90) REVERT: d 92 MET cc_start: 0.8460 (mtp) cc_final: 0.7902 (mmt) REVERT: d 97 VAL cc_start: 0.8696 (t) cc_final: 0.8268 (p) REVERT: d 98 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7694 (tm-30) REVERT: d 99 LEU cc_start: 0.7118 (mp) cc_final: 0.6916 (mt) REVERT: d 120 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8219 (tp) REVERT: e 92 GLN cc_start: 0.8745 (tt0) cc_final: 0.8286 (tt0) REVERT: e 123 MET cc_start: 0.8366 (pmm) cc_final: 0.8072 (pmm) REVERT: e 145 LEU cc_start: 0.8648 (mm) cc_final: 0.8112 (tt) REVERT: e 147 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8068 (mm) REVERT: f 101 ARG cc_start: 0.7349 (mmt90) cc_final: 0.7108 (mpt180) REVERT: f 104 LYS cc_start: 0.9195 (tmmt) cc_final: 0.8864 (ptmm) REVERT: f 121 ASN cc_start: 0.9229 (t0) cc_final: 0.8847 (t0) REVERT: f 125 MET cc_start: 0.6858 (pmm) cc_final: 0.6655 (pmm) REVERT: g 34 TYR cc_start: 0.8624 (t80) cc_final: 0.8167 (t80) REVERT: g 38 GLU cc_start: 0.8082 (pm20) cc_final: 0.7309 (pm20) REVERT: g 44 LEU cc_start: 0.8662 (tt) cc_final: 0.8222 (tp) REVERT: g 72 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.8151 (t-100) REVERT: g 73 ASN cc_start: 0.9477 (t0) cc_final: 0.9271 (t0) REVERT: g 82 ARG cc_start: 0.8741 (mmt90) cc_final: 0.8161 (mmt-90) REVERT: g 119 LEU cc_start: 0.9097 (tp) cc_final: 0.8797 (tp) REVERT: n 259 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7595 (t0) outliers start: 40 outliers final: 26 residues processed: 192 average time/residue: 0.1482 time to fit residues: 35.5740 Evaluate side-chains 191 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain f residue 75 ILE Chi-restraints excluded: chain g residue 72 TRP Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 284 THR Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Chi-restraints excluded: chain n residue 281 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN m 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4468 Z= 0.181 Angle : 0.680 7.848 6051 Z= 0.339 Chirality : 0.041 0.150 721 Planarity : 0.004 0.060 728 Dihedral : 7.148 55.867 658 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 8.76 % Allowed : 35.44 % Favored : 55.80 % 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: -0.06 (0.35), residues: 520 helix: 2.41 (0.32), residues: 215 sheet: -0.42 (0.69), residues: 62 loop : -2.39 (0.33), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 59 HIS 0.002 0.001 HIS g 29 PHE 0.019 0.002 PHE g 118 TYR 0.020 0.001 TYR a 42 ARG 0.003 0.000 ARG n 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 52 ARG cc_start: 0.6722 (ttt180) cc_final: 0.6279 (ttt180) REVERT: b 34 LEU cc_start: 0.7895 (tt) cc_final: 0.7272 (mm) REVERT: d 63 ARG cc_start: 0.8900 (ttm170) cc_final: 0.8237 (mtp-110) REVERT: d 72 ARG cc_start: 0.7506 (tpt-90) cc_final: 0.7014 (tpt-90) REVERT: d 79 TYR cc_start: 0.8126 (m-80) cc_final: 0.7898 (m-80) REVERT: d 92 MET cc_start: 0.8431 (mtp) cc_final: 0.7904 (mmt) REVERT: d 97 VAL cc_start: 0.8838 (t) cc_final: 0.8526 (p) REVERT: d 98 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8037 (tp30) REVERT: d 99 LEU cc_start: 0.6743 (mp) cc_final: 0.6172 (mt) REVERT: d 120 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8134 (tp) REVERT: e 87 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8092 (t80) REVERT: e 92 GLN cc_start: 0.8738 (tt0) cc_final: 0.8289 (tt0) REVERT: e 145 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8251 (tt) REVERT: e 147 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7910 (mm) REVERT: f 101 ARG cc_start: 0.7301 (mmt90) cc_final: 0.7089 (mpt180) REVERT: f 104 LYS cc_start: 0.9255 (tmmt) cc_final: 0.8716 (tmmt) REVERT: f 106 GLU cc_start: 0.8259 (mp0) cc_final: 0.7905 (mp0) REVERT: f 120 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8724 (tm-30) REVERT: f 121 ASN cc_start: 0.9226 (t0) cc_final: 0.8737 (t0) REVERT: f 125 MET cc_start: 0.6828 (pmm) cc_final: 0.6584 (pmm) REVERT: g 34 TYR cc_start: 0.8577 (t80) cc_final: 0.8318 (t80) REVERT: g 38 GLU cc_start: 0.8357 (pm20) cc_final: 0.8073 (pm20) REVERT: g 73 ASN cc_start: 0.9451 (t0) cc_final: 0.9236 (t0) REVERT: g 74 LEU cc_start: 0.8794 (tt) cc_final: 0.8246 (mt) REVERT: g 82 ARG cc_start: 0.8618 (mmt90) cc_final: 0.8203 (mmt-90) REVERT: g 84 MET cc_start: 0.4775 (mmm) cc_final: 0.4472 (mmm) REVERT: g 119 LEU cc_start: 0.9041 (tp) cc_final: 0.8716 (tp) REVERT: n 259 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7488 (t0) outliers start: 43 outliers final: 29 residues processed: 193 average time/residue: 0.1406 time to fit residues: 34.5009 Evaluate side-chains 192 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 45 GLU Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 137 ASP Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4468 Z= 0.208 Angle : 0.683 8.358 6051 Z= 0.341 Chirality : 0.042 0.173 721 Planarity : 0.004 0.043 728 Dihedral : 7.005 54.579 658 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 12.83 % Allowed : 32.38 % Favored : 54.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.35), residues: 520 helix: 2.31 (0.32), residues: 217 sheet: -0.32 (0.71), residues: 62 loop : -2.39 (0.33), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 59 HIS 0.002 0.001 HIS d 89 PHE 0.022 0.002 PHE a 40 TYR 0.019 0.001 TYR g 100 ARG 0.005 0.000 ARG g 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 158 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.4271 (t80) REVERT: a 52 ARG cc_start: 0.6852 (ttt180) cc_final: 0.6334 (ttt180) REVERT: b 34 LEU cc_start: 0.7842 (tt) cc_final: 0.7234 (mm) REVERT: d 63 ARG cc_start: 0.8978 (ttm170) cc_final: 0.8265 (mtp-110) REVERT: d 72 ARG cc_start: 0.7582 (tpt-90) cc_final: 0.7188 (tpt-90) REVERT: d 92 MET cc_start: 0.8462 (mtp) cc_final: 0.7972 (mmt) REVERT: d 97 VAL cc_start: 0.8698 (t) cc_final: 0.8486 (p) REVERT: d 98 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7592 (tp30) REVERT: d 99 LEU cc_start: 0.6908 (mp) cc_final: 0.6570 (mt) REVERT: d 120 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8216 (tp) REVERT: e 37 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8180 (ttpp) REVERT: e 87 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8100 (t80) REVERT: e 122 CYS cc_start: 0.6893 (t) cc_final: 0.6566 (t) REVERT: e 145 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8054 (tt) REVERT: e 147 LEU cc_start: 0.8190 (tt) cc_final: 0.7900 (mm) REVERT: f 104 LYS cc_start: 0.9325 (ttmt) cc_final: 0.8751 (tmmt) REVERT: f 106 GLU cc_start: 0.8284 (mp0) cc_final: 0.7993 (mp0) REVERT: f 121 ASN cc_start: 0.9193 (t0) cc_final: 0.8643 (t0) REVERT: f 125 MET cc_start: 0.6882 (pmm) cc_final: 0.6677 (pmm) REVERT: g 34 TYR cc_start: 0.8589 (t80) cc_final: 0.8291 (t80) REVERT: g 61 MET cc_start: 0.6803 (tpt) cc_final: 0.5107 (mmm) REVERT: g 119 LEU cc_start: 0.9082 (tp) cc_final: 0.8754 (tp) REVERT: m 272 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8360 (mp) REVERT: n 259 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7739 (t0) outliers start: 63 outliers final: 39 residues processed: 198 average time/residue: 0.1451 time to fit residues: 36.3872 Evaluate side-chains 197 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 66 ASP Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 269 LEU Chi-restraints excluded: chain m residue 272 LEU Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 284 THR Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Chi-restraints excluded: chain n residue 281 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.0000 chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 0.0070 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4468 Z= 0.173 Angle : 0.692 7.708 6051 Z= 0.339 Chirality : 0.041 0.149 721 Planarity : 0.003 0.038 728 Dihedral : 6.932 55.246 657 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 8.15 % Allowed : 37.88 % Favored : 53.97 % 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: -0.03 (0.35), residues: 520 helix: 2.34 (0.32), residues: 218 sheet: -0.26 (0.70), residues: 62 loop : -2.38 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP e 59 HIS 0.003 0.001 HIS e 61 PHE 0.021 0.002 PHE g 118 TYR 0.018 0.001 TYR g 100 ARG 0.003 0.000 ARG n 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6286 (OUTLIER) cc_final: 0.4454 (t80) REVERT: a 52 ARG cc_start: 0.6849 (ttt180) cc_final: 0.6333 (ttt180) REVERT: b 34 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7129 (mm) REVERT: b 40 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7878 (t80) REVERT: d 63 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8296 (mtp-110) REVERT: d 72 ARG cc_start: 0.7596 (tpt-90) cc_final: 0.7208 (tpt-90) REVERT: d 92 MET cc_start: 0.8460 (mtp) cc_final: 0.7957 (mmt) REVERT: d 97 VAL cc_start: 0.8717 (t) cc_final: 0.8335 (p) REVERT: d 98 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7782 (tp30) REVERT: d 120 LEU cc_start: 0.8340 (tt) cc_final: 0.8137 (tp) REVERT: e 87 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8118 (t80) REVERT: e 122 CYS cc_start: 0.6628 (t) cc_final: 0.6190 (t) REVERT: e 145 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8177 (tt) REVERT: e 147 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7908 (mm) REVERT: f 104 LYS cc_start: 0.9351 (ttmt) cc_final: 0.8510 (ttpp) REVERT: f 120 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8662 (tm-30) REVERT: f 121 ASN cc_start: 0.9214 (t0) cc_final: 0.8604 (t0) REVERT: f 128 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8073 (tmm) REVERT: g 34 TYR cc_start: 0.8561 (t80) cc_final: 0.8267 (t80) REVERT: g 38 GLU cc_start: 0.8396 (pm20) cc_final: 0.8167 (pm20) REVERT: g 61 MET cc_start: 0.6666 (tpt) cc_final: 0.5258 (mmm) REVERT: g 119 LEU cc_start: 0.9066 (tp) cc_final: 0.8734 (tp) REVERT: n 259 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7351 (t0) outliers start: 40 outliers final: 27 residues processed: 177 average time/residue: 0.1494 time to fit residues: 33.7038 Evaluate side-chains 179 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 32 CYS Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 147 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 128 MET Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4468 Z= 0.174 Angle : 0.688 8.058 6051 Z= 0.340 Chirality : 0.041 0.161 721 Planarity : 0.003 0.034 728 Dihedral : 6.653 54.139 655 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.55 % Allowed : 39.10 % Favored : 52.34 % 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: -0.19 (0.35), residues: 520 helix: 2.26 (0.32), residues: 219 sheet: -0.75 (0.64), residues: 71 loop : -2.46 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 59 HIS 0.002 0.001 HIS e 61 PHE 0.033 0.002 PHE a 40 TYR 0.020 0.001 TYR g 85 ARG 0.002 0.000 ARG n 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.4340 (t80) REVERT: a 52 ARG cc_start: 0.6751 (ttt180) cc_final: 0.6226 (ttt180) REVERT: b 34 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7141 (mm) REVERT: d 63 ARG cc_start: 0.8967 (ttm170) cc_final: 0.8291 (mtp-110) REVERT: d 72 ARG cc_start: 0.7589 (tpt-90) cc_final: 0.7294 (tpp80) REVERT: d 92 MET cc_start: 0.8479 (mtp) cc_final: 0.7958 (mmt) REVERT: d 97 VAL cc_start: 0.8745 (t) cc_final: 0.8500 (p) REVERT: d 98 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7868 (tm-30) REVERT: d 120 LEU cc_start: 0.8326 (tt) cc_final: 0.8123 (tp) REVERT: e 87 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8231 (t80) REVERT: e 115 ARG cc_start: 0.8099 (ttm110) cc_final: 0.7702 (ttp-110) REVERT: e 145 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8068 (tt) REVERT: e 147 LEU cc_start: 0.8215 (tt) cc_final: 0.7991 (mm) REVERT: f 104 LYS cc_start: 0.9188 (ttmt) cc_final: 0.8851 (ttpp) REVERT: f 110 PHE cc_start: 0.7003 (p90) cc_final: 0.6654 (p90) REVERT: f 112 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8597 (tp) REVERT: f 121 ASN cc_start: 0.9198 (t0) cc_final: 0.8667 (t0) REVERT: f 128 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8043 (tmm) REVERT: g 34 TYR cc_start: 0.8632 (t80) cc_final: 0.8333 (t80) REVERT: g 61 MET cc_start: 0.6754 (tpt) cc_final: 0.6306 (mmm) REVERT: g 82 ARG cc_start: 0.8629 (mmt90) cc_final: 0.8194 (mmt-90) REVERT: g 119 LEU cc_start: 0.9051 (tp) cc_final: 0.8746 (tp) REVERT: n 259 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7365 (t0) outliers start: 42 outliers final: 30 residues processed: 179 average time/residue: 0.1589 time to fit residues: 35.7861 Evaluate side-chains 185 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 40 PHE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 79 TYR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 128 MET Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 22 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4468 Z= 0.174 Angle : 0.694 7.692 6051 Z= 0.344 Chirality : 0.040 0.148 721 Planarity : 0.003 0.032 728 Dihedral : 6.499 53.266 655 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 8.55 % Allowed : 41.34 % Favored : 50.10 % 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: -0.17 (0.35), residues: 520 helix: 2.33 (0.32), residues: 218 sheet: -0.70 (0.64), residues: 71 loop : -2.50 (0.32), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 59 HIS 0.002 0.000 HIS e 61 PHE 0.022 0.001 PHE g 118 TYR 0.021 0.001 TYR g 85 ARG 0.002 0.000 ARG n 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.4339 (t80) REVERT: a 52 ARG cc_start: 0.6787 (ttt180) cc_final: 0.6236 (ttt180) REVERT: b 34 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7188 (mm) REVERT: d 63 ARG cc_start: 0.8979 (ttm170) cc_final: 0.8258 (mtp-110) REVERT: d 72 ARG cc_start: 0.7491 (tpt-90) cc_final: 0.7184 (tpt-90) REVERT: d 92 MET cc_start: 0.8494 (mtp) cc_final: 0.7947 (mmt) REVERT: d 98 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7309 (tp30) REVERT: d 120 LEU cc_start: 0.8331 (tt) cc_final: 0.8103 (tp) REVERT: e 87 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8267 (t80) REVERT: e 115 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7526 (ttp-110) REVERT: e 120 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7145 (tm-30) REVERT: e 145 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8208 (tt) REVERT: e 147 LEU cc_start: 0.8144 (tt) cc_final: 0.7914 (mm) REVERT: f 104 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8723 (ttpp) REVERT: f 110 PHE cc_start: 0.6961 (p90) cc_final: 0.6564 (p90) REVERT: f 112 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8584 (tp) REVERT: f 120 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8529 (tm-30) REVERT: f 121 ASN cc_start: 0.9244 (t0) cc_final: 0.8541 (t0) REVERT: g 34 TYR cc_start: 0.8662 (t80) cc_final: 0.8366 (t80) REVERT: g 61 MET cc_start: 0.6681 (tpt) cc_final: 0.6302 (mmm) REVERT: g 119 LEU cc_start: 0.9006 (tp) cc_final: 0.8690 (tp) REVERT: n 259 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7348 (t0) outliers start: 42 outliers final: 29 residues processed: 177 average time/residue: 0.1568 time to fit residues: 34.8264 Evaluate side-chains 182 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4468 Z= 0.229 Angle : 0.727 8.006 6051 Z= 0.360 Chirality : 0.043 0.263 721 Planarity : 0.003 0.028 728 Dihedral : 6.553 51.936 655 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 9.78 % Allowed : 41.34 % Favored : 48.88 % 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: -0.30 (0.35), residues: 520 helix: 2.14 (0.32), residues: 222 sheet: -0.66 (0.65), residues: 71 loop : -2.61 (0.32), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP e 59 HIS 0.002 0.001 HIS f 61 PHE 0.022 0.002 PHE g 118 TYR 0.016 0.001 TYR f 149 ARG 0.005 0.000 ARG g 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 150 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5084 (t80) REVERT: a 46 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7078 (tt) REVERT: a 52 ARG cc_start: 0.6933 (ttt180) cc_final: 0.6206 (ttt180) REVERT: b 34 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7263 (mm) REVERT: d 63 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8271 (mtp-110) REVERT: d 72 ARG cc_start: 0.7475 (tpt-90) cc_final: 0.7247 (tpt-90) REVERT: d 92 MET cc_start: 0.8556 (mtp) cc_final: 0.8092 (mmt) REVERT: d 98 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7797 (tm-30) REVERT: d 120 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8172 (tp) REVERT: e 87 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8291 (t80) REVERT: e 145 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8041 (tt) REVERT: e 147 LEU cc_start: 0.8218 (tt) cc_final: 0.7909 (mm) REVERT: f 104 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8858 (ttpp) REVERT: f 110 PHE cc_start: 0.7107 (p90) cc_final: 0.6680 (p90) REVERT: f 121 ASN cc_start: 0.9193 (t0) cc_final: 0.8509 (t0) REVERT: g 34 TYR cc_start: 0.8666 (t80) cc_final: 0.8358 (t80) REVERT: g 74 LEU cc_start: 0.8990 (tt) cc_final: 0.8557 (mt) REVERT: g 119 LEU cc_start: 0.9056 (tp) cc_final: 0.8725 (tp) REVERT: m 286 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8069 (tptp) REVERT: n 259 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.7685 (t0) outliers start: 48 outliers final: 34 residues processed: 180 average time/residue: 0.1373 time to fit residues: 31.6739 Evaluate side-chains 187 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 87 PHE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 90 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 128 MET Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4468 Z= 0.190 Angle : 0.735 8.445 6051 Z= 0.361 Chirality : 0.041 0.183 721 Planarity : 0.003 0.027 728 Dihedral : 6.635 53.015 655 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 8.55 % Allowed : 41.75 % Favored : 49.69 % 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: -0.23 (0.35), residues: 520 helix: 2.23 (0.32), residues: 222 sheet: -0.64 (0.64), residues: 71 loop : -2.60 (0.31), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 59 HIS 0.003 0.001 HIS e 61 PHE 0.023 0.002 PHE g 118 TYR 0.016 0.001 TYR a 42 ARG 0.002 0.000 ARG d 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 152 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.5115 (t80) REVERT: a 46 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7125 (tt) REVERT: a 52 ARG cc_start: 0.6834 (ttt180) cc_final: 0.6131 (ttt180) REVERT: b 34 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7291 (mm) REVERT: d 63 ARG cc_start: 0.8970 (ttm170) cc_final: 0.8240 (mtp-110) REVERT: d 92 MET cc_start: 0.8559 (mtp) cc_final: 0.8059 (mmt) REVERT: d 98 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7391 (tp30) REVERT: d 120 LEU cc_start: 0.8367 (tt) cc_final: 0.8151 (tp) REVERT: e 115 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7515 (ttp-110) REVERT: e 145 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8117 (tt) REVERT: e 147 LEU cc_start: 0.8172 (tt) cc_final: 0.7931 (mm) REVERT: f 104 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8988 (ttpt) REVERT: f 110 PHE cc_start: 0.7162 (p90) cc_final: 0.6714 (p90) REVERT: f 121 ASN cc_start: 0.9222 (t0) cc_final: 0.8215 (t0) REVERT: g 34 TYR cc_start: 0.8667 (t80) cc_final: 0.8368 (t80) REVERT: g 119 LEU cc_start: 0.9074 (tp) cc_final: 0.8771 (tp) REVERT: m 286 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7934 (tptp) REVERT: n 259 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7401 (t0) outliers start: 42 outliers final: 30 residues processed: 178 average time/residue: 0.1488 time to fit residues: 33.3993 Evaluate side-chains 184 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Chi-restraints excluded: chain n residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4468 Z= 0.201 Angle : 0.736 8.430 6051 Z= 0.363 Chirality : 0.041 0.185 721 Planarity : 0.003 0.027 728 Dihedral : 6.441 50.985 655 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 8.35 % Allowed : 42.77 % Favored : 48.88 % 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: -0.22 (0.35), residues: 520 helix: 2.26 (0.32), residues: 219 sheet: -0.64 (0.65), residues: 71 loop : -2.55 (0.31), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 59 HIS 0.001 0.000 HIS f 81 PHE 0.024 0.002 PHE g 118 TYR 0.015 0.001 TYR a 42 ARG 0.003 0.000 ARG e 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 148 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 42 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6168 (t80) REVERT: a 46 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7113 (tt) REVERT: a 52 ARG cc_start: 0.6891 (ttt180) cc_final: 0.6160 (ttt180) REVERT: b 34 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7434 (mm) REVERT: d 63 ARG cc_start: 0.9008 (ttm170) cc_final: 0.8270 (mtp-110) REVERT: d 72 ARG cc_start: 0.7454 (tpt-90) cc_final: 0.7178 (tpp-160) REVERT: d 92 MET cc_start: 0.8503 (mtp) cc_final: 0.8069 (mmt) REVERT: d 120 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8169 (tp) REVERT: e 145 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8032 (tt) REVERT: e 147 LEU cc_start: 0.8200 (tt) cc_final: 0.7904 (mm) REVERT: f 104 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8849 (ttpp) REVERT: f 110 PHE cc_start: 0.7294 (p90) cc_final: 0.6847 (p90) REVERT: f 121 ASN cc_start: 0.9174 (t0) cc_final: 0.8185 (t0) REVERT: g 34 TYR cc_start: 0.8670 (t80) cc_final: 0.8446 (t80) REVERT: g 74 LEU cc_start: 0.9001 (tt) cc_final: 0.8581 (mt) REVERT: g 119 LEU cc_start: 0.9117 (tp) cc_final: 0.8779 (tp) REVERT: m 286 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7953 (tptp) REVERT: n 259 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7517 (t0) outliers start: 41 outliers final: 31 residues processed: 175 average time/residue: 0.1432 time to fit residues: 31.6387 Evaluate side-chains 182 residues out of total 491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 TYR Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 110 PHE Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain f residue 77 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 144 LEU Chi-restraints excluded: chain f residue 147 LEU Chi-restraints excluded: chain m residue 264 LEU Chi-restraints excluded: chain m residue 266 VAL Chi-restraints excluded: chain m residue 276 THR Chi-restraints excluded: chain m residue 277 VAL Chi-restraints excluded: chain m residue 279 VAL Chi-restraints excluded: chain m residue 283 LEU Chi-restraints excluded: chain m residue 286 LYS Chi-restraints excluded: chain n residue 257 LEU Chi-restraints excluded: chain n residue 259 ASN Chi-restraints excluded: chain n residue 274 VAL Chi-restraints excluded: chain n residue 280 ILE Chi-restraints excluded: chain n residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.135994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104174 restraints weight = 9941.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.107333 restraints weight = 6816.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108390 restraints weight = 4428.878| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4468 Z= 0.232 Angle : 0.767 8.209 6051 Z= 0.377 Chirality : 0.042 0.206 721 Planarity : 0.003 0.025 728 Dihedral : 6.509 50.504 655 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 8.55 % Allowed : 42.97 % Favored : 48.47 % 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: -0.23 (0.35), residues: 520 helix: 2.25 (0.32), residues: 222 sheet: -0.67 (0.66), residues: 71 loop : -2.60 (0.31), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP e 59 HIS 0.001 0.000 HIS f 81 PHE 0.023 0.002 PHE g 118 TYR 0.015 0.001 TYR a 42 ARG 0.003 0.000 ARG g 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1337.95 seconds wall clock time: 24 minutes 24.91 seconds (1464.91 seconds total)