Starting phenix.real_space_refine on Mon Apr 8 07:33:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfm_33176/04_2024/7xfm_33176_updated.pdb" } resolution = 3.1 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 265 5.49 5 S 21 5.16 5 C 7286 2.51 5 N 2419 2.21 5 O 2923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12914 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2730 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2710 Classifications: {'DNA': 133} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 132} Chain: "K" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1566 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain breaks: 2 Time building chain proxies: 7.13, per 1000 atoms: 0.55 Number of scatterers: 12914 At special positions: 0 Unit cell: (138.864, 115.72, 100.992, 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 21 16.00 P 265 15.00 O 2923 8.00 N 2419 7.00 C 7286 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: 6.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 4 sheets defined 53.5% alpha, 3.4% beta 118 base pairs and 230 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.840A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.516A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 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 120 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.667A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.047A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (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 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 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.727A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 36 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 88 through 91 No H-bonds generated for 'chain 'K' and resid 88 through 91' Processing helix chain 'K' and resid 95 through 100 Processing helix chain 'K' and resid 190 through 197 Processing helix chain 'K' and resid 218 through 222 Processing sheet with id= A, first strand: chain 'K' and resid 106 through 108 Processing sheet with id= B, first strand: chain 'K' and resid 124 through 127 removed outlier: 4.692A pdb=" N MET K 168 " --> pdb=" O LEU K 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 255 through 259 removed outlier: 4.310A pdb=" N ALA K 255 " --> pdb=" O ARG K 280 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG K 276 " --> pdb=" O ALA K 259 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 120 through 123 removed outlier: 6.832A pdb=" N ALA K 183 " --> pdb=" O VAL K 122 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 612 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 230 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2844 1.33 - 1.46: 4361 1.46 - 1.58: 5912 1.58 - 1.70: 530 1.70 - 1.82: 36 Bond restraints: 13683 Sorted by residual: bond pdb=" C2' AAB I -53 " pdb=" C1' AAB I -53 " ideal model delta sigma weight residual 1.341 1.522 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" O4' AAB I -53 " pdb=" C1' AAB I -53 " ideal model delta sigma weight residual 1.601 1.430 0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" C4' AAB I -53 " pdb=" O4' AAB I -53 " ideal model delta sigma weight residual 1.293 1.430 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C ILE K 161 " pdb=" N TYR K 162 " ideal model delta sigma weight residual 1.332 1.419 -0.086 1.40e-02 5.10e+03 3.79e+01 bond pdb=" C3' AAB I -53 " pdb=" O3' AAB I -53 " ideal model delta sigma weight residual 1.362 1.448 -0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 13678 not shown) Histogram of bond angle deviations from ideal: 79.75 - 90.91: 2 90.91 - 102.08: 254 102.08 - 113.25: 8761 113.25 - 124.42: 9538 124.42 - 135.59: 1061 Bond angle restraints: 19616 Sorted by residual: angle pdb=" O3' DA J 57 " pdb=" P DG J 58 " pdb=" OP1 DG J 58 " ideal model delta sigma weight residual 108.00 79.75 28.25 3.00e+00 1.11e-01 8.87e+01 angle pdb=" O3' DA J 57 " pdb=" P DG J 58 " pdb=" OP2 DG J 58 " ideal model delta sigma weight residual 108.00 90.43 17.57 3.00e+00 1.11e-01 3.43e+01 angle pdb=" CA ARG A 52 " pdb=" CB ARG A 52 " pdb=" CG ARG A 52 " ideal model delta sigma weight residual 114.10 124.86 -10.76 2.00e+00 2.50e-01 2.89e+01 angle pdb=" O3' DA J 57 " pdb=" P DG J 58 " pdb=" O5' DG J 58 " ideal model delta sigma weight residual 104.00 98.48 5.52 1.50e+00 4.44e-01 1.35e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 121.53 -8.35 2.37e+00 1.78e-01 1.24e+01 ... (remaining 19611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 6251 35.64 - 71.27: 1269 71.27 - 106.90: 16 106.90 - 142.54: 2 142.54 - 178.17: 4 Dihedral angle restraints: 7542 sinusoidal: 4817 harmonic: 2725 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.17 -178.17 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 55 " pdb=" C3' DT J 55 " pdb=" O3' DT J 55 " pdb=" P DC J 56 " ideal model delta sinusoidal sigma weight residual -140.00 35.84 -175.84 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.440: 2223 0.440 - 0.880: 0 0.880 - 1.320: 0 1.320 - 1.760: 0 1.760 - 2.199: 1 Chirality restraints: 2224 Sorted by residual: chirality pdb=" P DG J 58 " pdb=" OP1 DG J 58 " pdb=" OP2 DG J 58 " pdb=" O5' DG J 58 " both_signs ideal model delta sigma weight residual True 2.35 0.15 2.20 2.00e-01 2.50e+01 1.21e+02 chirality pdb=" CG LEU D 42 " pdb=" CB LEU D 42 " pdb=" CD1 LEU D 42 " pdb=" CD2 LEU D 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB VAL G 100 " pdb=" CA VAL G 100 " pdb=" CG1 VAL G 100 " pdb=" CG2 VAL G 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2221 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.08e+00 pdb=" N PRO C 80 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 57 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C VAL B 57 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL B 57 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 58 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 28 " 0.032 2.00e-02 2.50e+03 1.46e-02 5.82e+00 pdb=" N9 DA I 28 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DA I 28 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 28 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 28 " 0.010 2.00e-02 2.50e+03 pdb=" N6 DA I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 28 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 28 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 28 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 28 " -0.005 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3517 2.84 - 3.35: 10503 3.35 - 3.87: 24843 3.87 - 4.38: 28275 4.38 - 4.90: 41190 Nonbonded interactions: 108328 Sorted by model distance: nonbonded pdb=" O GLN K 93 " pdb=" OG SER K 172 " model vdw 2.322 2.440 nonbonded pdb=" NH2 ARG K 234 " pdb=" O GLN K 238 " model vdw 2.355 2.520 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.368 2.440 nonbonded pdb=" NH1 ARG E 116 " pdb=" O THR E 118 " model vdw 2.381 2.520 nonbonded pdb=" NH1 ARG D 83 " pdb=" OE2 GLU D 90 " model vdw 2.398 2.520 ... (remaining 108323 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 41 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 2.560 Check model and map are aligned: 0.200 Set scattering table: 0.160 Process input model: 43.260 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 : 0.007 0.181 13683 Z= 0.379 Angle : 0.848 28.254 19616 Z= 0.458 Chirality : 0.068 2.199 2224 Planarity : 0.007 0.071 1576 Dihedral : 26.709 178.173 5788 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.74 % 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 (0.24), residues: 924 helix: -0.69 (0.18), residues: 563 sheet: -2.44 (0.68), residues: 40 loop : -1.42 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 243 HIS 0.013 0.002 HIS D 46 PHE 0.027 0.002 PHE C 25 TYR 0.019 0.002 TYR E 54 ARG 0.026 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8125 (mttt) cc_final: 0.7795 (mttt) REVERT: A 80 THR cc_start: 0.8223 (p) cc_final: 0.7982 (p) REVERT: B 79 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7370 (mmtt) REVERT: B 84 MET cc_start: 0.8243 (tpt) cc_final: 0.7941 (tpp) REVERT: B 91 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7904 (ttpt) REVERT: C 20 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7211 (mtm-85) REVERT: C 74 LYS cc_start: 0.8007 (mttm) cc_final: 0.7447 (mtmt) REVERT: D 33 SER cc_start: 0.9168 (p) cc_final: 0.8756 (m) REVERT: E 49 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7573 (mtm110) REVERT: E 115 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8075 (mmtm) REVERT: F 77 LYS cc_start: 0.8049 (mtpp) cc_final: 0.7835 (mttt) REVERT: F 79 LYS cc_start: 0.8101 (mttp) cc_final: 0.7883 (mttt) REVERT: F 91 LYS cc_start: 0.8277 (tttt) cc_final: 0.8012 (ttmt) REVERT: G 15 LYS cc_start: 0.7140 (mtpp) cc_final: 0.6725 (mttt) REVERT: G 36 LYS cc_start: 0.7569 (mppt) cc_final: 0.7363 (mtpp) REVERT: G 75 LYS cc_start: 0.8062 (mttt) cc_final: 0.7862 (mttm) REVERT: K 261 ARG cc_start: 0.1412 (mpt-90) cc_final: 0.1211 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.5129 time to fit residues: 106.1215 Evaluate side-chains 101 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN B 25 ASN C 24 GLN C 104 GLN D 92 GLN F 25 ASN K 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13683 Z= 0.230 Angle : 0.629 26.748 19616 Z= 0.342 Chirality : 0.056 2.049 2224 Planarity : 0.005 0.050 1576 Dihedral : 29.893 177.553 3945 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.15 % Allowed : 8.07 % Favored : 90.78 % 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: -0.13 (0.26), residues: 924 helix: 0.76 (0.21), residues: 562 sheet: -2.37 (0.71), residues: 40 loop : -1.21 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 243 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE C 25 TYR 0.015 0.002 TYR K 162 ARG 0.005 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8083 (mttm) cc_final: 0.7731 (mtpt) REVERT: A 64 LYS cc_start: 0.8175 (mttt) cc_final: 0.7964 (mttt) REVERT: A 80 THR cc_start: 0.8289 (p) cc_final: 0.8013 (p) REVERT: B 79 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7730 (mttp) REVERT: B 84 MET cc_start: 0.8418 (tpt) cc_final: 0.8178 (mmt) REVERT: B 91 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7949 (ttpt) REVERT: C 20 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7206 (mtm-85) REVERT: C 59 THR cc_start: 0.8952 (t) cc_final: 0.8665 (m) REVERT: C 74 LYS cc_start: 0.8059 (mttm) cc_final: 0.7347 (mttt) REVERT: E 49 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7456 (mtm110) REVERT: E 115 LYS cc_start: 0.8364 (mmtp) cc_final: 0.8132 (mmtm) REVERT: F 77 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7839 (mttt) REVERT: G 15 LYS cc_start: 0.7009 (mtpp) cc_final: 0.6678 (mttt) REVERT: G 36 LYS cc_start: 0.7497 (mppt) cc_final: 0.7203 (mtpp) REVERT: G 72 ASP cc_start: 0.7921 (m-30) cc_final: 0.7666 (m-30) REVERT: G 75 LYS cc_start: 0.8237 (mttt) cc_final: 0.7926 (mttm) REVERT: G 95 LYS cc_start: 0.8409 (pttt) cc_final: 0.8105 (pttt) REVERT: H 56 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8420 (tpt) outliers start: 9 outliers final: 7 residues processed: 117 average time/residue: 0.3709 time to fit residues: 57.3548 Evaluate side-chains 101 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 115 optimal weight: 0.0870 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13683 Z= 0.324 Angle : 0.668 26.821 19616 Z= 0.362 Chirality : 0.059 2.072 2224 Planarity : 0.005 0.044 1576 Dihedral : 30.097 179.005 3945 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.54 % Allowed : 13.44 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.27), residues: 924 helix: 0.95 (0.21), residues: 565 sheet: -2.57 (0.69), residues: 40 loop : -1.19 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 243 HIS 0.005 0.001 HIS D 46 PHE 0.016 0.002 PHE C 25 TYR 0.016 0.002 TYR A 54 ARG 0.004 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8131 (mttm) cc_final: 0.7798 (mtpt) REVERT: B 49 LEU cc_start: 0.9094 (mt) cc_final: 0.8848 (mp) REVERT: B 79 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7617 (mptt) REVERT: B 91 LYS cc_start: 0.8441 (ttpt) cc_final: 0.7942 (ttpt) REVERT: C 41 GLU cc_start: 0.7757 (tt0) cc_final: 0.7557 (tt0) REVERT: C 59 THR cc_start: 0.8856 (t) cc_final: 0.8567 (m) REVERT: C 74 LYS cc_start: 0.8158 (mttm) cc_final: 0.7458 (mttt) REVERT: D 56 MET cc_start: 0.8553 (tpp) cc_final: 0.7898 (tpp) REVERT: F 31 LYS cc_start: 0.8024 (tttt) cc_final: 0.7751 (ttpt) REVERT: F 77 LYS cc_start: 0.8004 (mtpp) cc_final: 0.7700 (mttt) REVERT: F 93 GLN cc_start: 0.7880 (mp10) cc_final: 0.7634 (mt0) REVERT: G 15 LYS cc_start: 0.6982 (mtpp) cc_final: 0.6672 (mttt) REVERT: G 36 LYS cc_start: 0.7576 (mppt) cc_final: 0.7292 (mmmt) REVERT: G 75 LYS cc_start: 0.8274 (mttt) cc_final: 0.7930 (mttm) REVERT: H 65 ASP cc_start: 0.8786 (t0) cc_final: 0.8581 (t0) outliers start: 12 outliers final: 8 residues processed: 117 average time/residue: 0.3277 time to fit residues: 52.1006 Evaluate side-chains 110 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13683 Z= 0.285 Angle : 0.640 26.828 19616 Z= 0.350 Chirality : 0.058 2.065 2224 Planarity : 0.004 0.042 1576 Dihedral : 30.035 177.421 3945 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.05 % Allowed : 14.98 % Favored : 82.97 % 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: 0.35 (0.27), residues: 924 helix: 1.24 (0.21), residues: 564 sheet: -2.72 (0.65), residues: 40 loop : -1.15 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 243 HIS 0.005 0.001 HIS B 75 PHE 0.013 0.002 PHE G 25 TYR 0.014 0.002 TYR A 54 ARG 0.008 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8064 (mttm) cc_final: 0.7089 (mmtt) REVERT: A 65 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7443 (mp) REVERT: B 79 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7552 (mptt) REVERT: B 91 LYS cc_start: 0.8460 (ttpt) cc_final: 0.7979 (ttpt) REVERT: C 59 THR cc_start: 0.8858 (t) cc_final: 0.8561 (m) REVERT: C 74 LYS cc_start: 0.8083 (mttm) cc_final: 0.7456 (mttt) REVERT: F 31 LYS cc_start: 0.8094 (tttt) cc_final: 0.7779 (ttpt) REVERT: F 77 LYS cc_start: 0.8058 (mtpp) cc_final: 0.7768 (mttt) REVERT: G 15 LYS cc_start: 0.7109 (mtpp) cc_final: 0.6705 (mttt) REVERT: G 36 LYS cc_start: 0.7693 (mppt) cc_final: 0.7429 (mtpp) REVERT: G 75 LYS cc_start: 0.8284 (mttt) cc_final: 0.7953 (mttm) REVERT: H 65 ASP cc_start: 0.8718 (t0) cc_final: 0.8485 (t0) outliers start: 16 outliers final: 13 residues processed: 114 average time/residue: 0.3369 time to fit residues: 51.7742 Evaluate side-chains 109 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 0.0170 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13683 Z= 0.299 Angle : 0.648 26.750 19616 Z= 0.354 Chirality : 0.058 2.074 2224 Planarity : 0.004 0.042 1576 Dihedral : 30.081 178.609 3945 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.18 % Allowed : 16.01 % Favored : 81.82 % 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: 0.44 (0.27), residues: 924 helix: 1.33 (0.21), residues: 564 sheet: -2.86 (0.64), residues: 40 loop : -1.12 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 243 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE G 25 TYR 0.014 0.002 TYR A 54 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8047 (mttm) cc_final: 0.7711 (mtpt) REVERT: A 65 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 63 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 79 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7455 (mptt) REVERT: C 59 THR cc_start: 0.8842 (t) cc_final: 0.8537 (m) REVERT: C 74 LYS cc_start: 0.8087 (mttm) cc_final: 0.7438 (mttt) REVERT: D 56 MET cc_start: 0.8472 (tpp) cc_final: 0.7933 (tpp) REVERT: F 31 LYS cc_start: 0.8093 (tttt) cc_final: 0.7769 (ttpt) REVERT: F 77 LYS cc_start: 0.8098 (mtpp) cc_final: 0.7799 (mtmt) REVERT: F 93 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: G 15 LYS cc_start: 0.7100 (mtpp) cc_final: 0.6687 (mttt) REVERT: G 36 LYS cc_start: 0.7679 (mppt) cc_final: 0.7397 (mtpp) REVERT: G 75 LYS cc_start: 0.8309 (mttt) cc_final: 0.7965 (mttm) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.3243 time to fit residues: 47.5985 Evaluate side-chains 108 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 158 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13683 Z= 0.264 Angle : 0.632 26.756 19616 Z= 0.347 Chirality : 0.058 2.070 2224 Planarity : 0.004 0.042 1576 Dihedral : 30.062 178.536 3945 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.94 % Allowed : 16.39 % Favored : 80.67 % 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: 0.62 (0.27), residues: 924 helix: 1.49 (0.22), residues: 564 sheet: -2.85 (0.63), residues: 40 loop : -1.09 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 243 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE G 25 TYR 0.013 0.002 TYR E 54 ARG 0.005 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8033 (mttm) cc_final: 0.7700 (mtpt) REVERT: A 65 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7496 (mp) REVERT: B 79 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7548 (mptt) REVERT: C 59 THR cc_start: 0.8849 (t) cc_final: 0.8565 (m) REVERT: C 74 LYS cc_start: 0.8089 (mttm) cc_final: 0.7434 (mttt) REVERT: D 56 MET cc_start: 0.8534 (tpp) cc_final: 0.8005 (tpp) REVERT: D 89 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6940 (ttp80) REVERT: F 31 LYS cc_start: 0.8090 (tttt) cc_final: 0.7768 (ttpt) REVERT: F 77 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7794 (mtmt) REVERT: F 93 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: G 15 LYS cc_start: 0.7094 (mtpp) cc_final: 0.6680 (mttt) REVERT: G 36 LYS cc_start: 0.7681 (mppt) cc_final: 0.7391 (mtpp) REVERT: G 75 LYS cc_start: 0.8298 (mttt) cc_final: 0.7951 (mttm) REVERT: G 95 LYS cc_start: 0.8604 (pttt) cc_final: 0.8172 (pttt) outliers start: 23 outliers final: 17 residues processed: 113 average time/residue: 0.3151 time to fit residues: 49.5861 Evaluate side-chains 115 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 179 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 0.0970 chunk 113 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13683 Z= 0.247 Angle : 0.623 26.798 19616 Z= 0.341 Chirality : 0.057 2.065 2224 Planarity : 0.004 0.041 1576 Dihedral : 29.999 178.318 3945 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.94 % Allowed : 16.77 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.27), residues: 924 helix: 1.60 (0.22), residues: 564 sheet: -2.86 (0.63), residues: 40 loop : -1.03 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 243 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE G 25 TYR 0.013 0.001 TYR E 54 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8007 (mttm) cc_final: 0.7692 (mtpt) REVERT: A 65 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7480 (mp) REVERT: B 63 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7672 (mt-10) REVERT: B 79 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7550 (mptt) REVERT: C 59 THR cc_start: 0.8849 (t) cc_final: 0.8579 (m) REVERT: C 74 LYS cc_start: 0.8060 (mttm) cc_final: 0.7395 (mttt) REVERT: D 89 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7092 (ttp80) REVERT: F 31 LYS cc_start: 0.8089 (tttt) cc_final: 0.7773 (ttpt) REVERT: F 77 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7831 (mtmt) REVERT: F 93 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: G 15 LYS cc_start: 0.7117 (mtpp) cc_final: 0.6682 (mttt) REVERT: G 36 LYS cc_start: 0.7618 (mppt) cc_final: 0.7318 (mtpp) REVERT: G 75 LYS cc_start: 0.8287 (mttt) cc_final: 0.7936 (mttm) REVERT: G 95 LYS cc_start: 0.8623 (pttt) cc_final: 0.8193 (pttt) outliers start: 23 outliers final: 18 residues processed: 114 average time/residue: 0.3237 time to fit residues: 50.8572 Evaluate side-chains 117 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.0570 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13683 Z= 0.182 Angle : 0.607 26.791 19616 Z= 0.334 Chirality : 0.056 2.054 2224 Planarity : 0.004 0.043 1576 Dihedral : 29.984 178.071 3945 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.43 % Allowed : 17.80 % Favored : 79.77 % 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: 0.98 (0.27), residues: 924 helix: 1.80 (0.22), residues: 564 sheet: -2.88 (0.62), residues: 40 loop : -0.97 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 243 HIS 0.005 0.001 HIS B 75 PHE 0.006 0.001 PHE G 25 TYR 0.011 0.001 TYR E 54 ARG 0.003 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7994 (mttm) cc_final: 0.7687 (mtpt) REVERT: A 65 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7457 (mp) REVERT: B 79 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7549 (mptt) REVERT: C 59 THR cc_start: 0.8833 (t) cc_final: 0.8583 (m) REVERT: C 74 LYS cc_start: 0.8059 (mttm) cc_final: 0.7388 (mttt) REVERT: D 89 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6975 (ttp80) REVERT: F 31 LYS cc_start: 0.8073 (tttt) cc_final: 0.7764 (ttpt) REVERT: F 77 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7801 (mttt) REVERT: F 93 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: G 15 LYS cc_start: 0.7105 (mtpp) cc_final: 0.6678 (mttt) REVERT: G 36 LYS cc_start: 0.7602 (mppt) cc_final: 0.7301 (mtpp) REVERT: G 75 LYS cc_start: 0.8265 (mttt) cc_final: 0.7917 (mttm) REVERT: G 95 LYS cc_start: 0.8604 (pttt) cc_final: 0.8175 (pttt) outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.3108 time to fit residues: 47.0393 Evaluate side-chains 116 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 179 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 0.0870 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13683 Z= 0.194 Angle : 0.606 26.798 19616 Z= 0.333 Chirality : 0.056 2.057 2224 Planarity : 0.004 0.042 1576 Dihedral : 29.941 178.215 3945 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.56 % Allowed : 17.67 % Favored : 79.77 % 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: 1.07 (0.28), residues: 924 helix: 1.87 (0.22), residues: 563 sheet: -2.86 (0.63), residues: 40 loop : -0.91 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 243 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE G 25 TYR 0.011 0.001 TYR E 54 ARG 0.004 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7987 (mttm) cc_final: 0.7677 (mtpt) REVERT: A 65 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7491 (mp) REVERT: B 79 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7552 (mptt) REVERT: C 59 THR cc_start: 0.8843 (t) cc_final: 0.8588 (m) REVERT: C 74 LYS cc_start: 0.8058 (mttm) cc_final: 0.7392 (mttt) REVERT: D 89 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7010 (ttp80) REVERT: F 31 LYS cc_start: 0.8077 (tttt) cc_final: 0.7766 (ttpt) REVERT: F 77 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7806 (mttt) REVERT: F 93 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: G 15 LYS cc_start: 0.7120 (mtpp) cc_final: 0.6680 (mttt) REVERT: G 36 LYS cc_start: 0.7599 (mppt) cc_final: 0.7300 (mtpp) REVERT: G 75 LYS cc_start: 0.8261 (mttt) cc_final: 0.7910 (mttm) REVERT: G 95 LYS cc_start: 0.8577 (pttt) cc_final: 0.8151 (pttt) outliers start: 20 outliers final: 16 residues processed: 111 average time/residue: 0.3060 time to fit residues: 47.2805 Evaluate side-chains 116 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 117 optimal weight: 0.0270 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 0.0570 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 1.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13683 Z= 0.194 Angle : 0.603 26.799 19616 Z= 0.331 Chirality : 0.056 2.057 2224 Planarity : 0.004 0.042 1576 Dihedral : 29.916 178.166 3945 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.18 % Allowed : 18.05 % Favored : 79.77 % 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: 1.11 (0.28), residues: 924 helix: 1.90 (0.22), residues: 563 sheet: -2.86 (0.63), residues: 40 loop : -0.89 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 243 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE G 25 TYR 0.014 0.001 TYR E 54 ARG 0.003 0.000 ARG A 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1848 Ramachandran restraints generated. 924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7985 (mttm) cc_final: 0.7676 (mtpt) REVERT: A 65 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7507 (mp) REVERT: B 79 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7557 (mptt) REVERT: C 59 THR cc_start: 0.8836 (t) cc_final: 0.8591 (m) REVERT: C 74 LYS cc_start: 0.7985 (mttm) cc_final: 0.7391 (mttt) REVERT: D 89 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7102 (ttp80) REVERT: F 31 LYS cc_start: 0.8075 (tttt) cc_final: 0.7767 (ttpt) REVERT: F 77 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7807 (mttt) REVERT: F 93 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: G 15 LYS cc_start: 0.7131 (mtpp) cc_final: 0.6713 (mttt) REVERT: G 36 LYS cc_start: 0.7600 (mppt) cc_final: 0.7300 (mtpp) REVERT: G 75 LYS cc_start: 0.8255 (mttt) cc_final: 0.7904 (mttm) REVERT: G 95 LYS cc_start: 0.8575 (pttt) cc_final: 0.8138 (pttt) outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.3087 time to fit residues: 47.1254 Evaluate side-chains 114 residues out of total 781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.181343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132244 restraints weight = 15329.132| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.28 r_work: 0.3093 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13683 Z= 0.295 Angle : 0.640 26.866 19616 Z= 0.350 Chirality : 0.058 2.071 2224 Planarity : 0.004 0.042 1576 Dihedral : 30.026 178.382 3945 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.56 % Allowed : 17.93 % Favored : 79.51 % 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: 0.80 (0.28), residues: 924 helix: 1.63 (0.22), residues: 570 sheet: -2.60 (0.61), residues: 51 loop : -1.00 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 243 HIS 0.005 0.001 HIS D 46 PHE 0.010 0.002 PHE G 25 TYR 0.015 0.002 TYR E 54 ARG 0.004 0.000 ARG E 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.60 seconds wall clock time: 44 minutes 48.95 seconds (2688.95 seconds total)