Starting phenix.real_space_refine on Fri Mar 15 22:20:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xfh_33172/03_2024/7xfh_33172_updated.pdb" } resolution = 2.9 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 263 5.49 5 S 21 5.16 5 C 7323 2.51 5 N 2437 2.21 5 O 2925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12969 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: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2709 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "J" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2690 Classifications: {'DNA': 132} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 131} 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: 6.73, per 1000 atoms: 0.52 Number of scatterers: 12969 At special positions: 0 Unit cell: (117.824, 115.72, 133.604, 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 263 15.00 O 2925 8.00 N 2437 7.00 C 7323 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: 6.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 4 sheets defined 52.2% alpha, 3.6% beta 124 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.101A 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: 3.808A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.367A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.642A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 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 35 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.343A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 119 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 224 Processing helix chain 'K' and resid 229 through 231 No H-bonds generated for 'chain 'K' and resid 229 through 231' 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: 4.814A pdb=" N MET K 168 " --> pdb=" O LEU K 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 256 through 259 removed outlier: 3.800A pdb=" N ARG K 276 " --> pdb=" O ALA K 259 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 119 through 123 removed outlier: 6.855A pdb=" N ALA K 183 " --> pdb=" O VAL K 122 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 322 hydrogen bonds 644 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 6.67 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: 2528 1.33 - 1.45: 4244 1.45 - 1.57: 6401 1.57 - 1.69: 525 1.69 - 1.81: 36 Bond restraints: 13734 Sorted by residual: bond pdb=" C2' AAB I -30 " pdb=" C1' AAB I -30 " ideal model delta sigma weight residual 1.341 1.521 -0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" O4' AAB I -30 " pdb=" C1' AAB I -30 " ideal model delta sigma weight residual 1.601 1.429 0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" C4' AAB I -30 " pdb=" O4' AAB I -30 " ideal model delta sigma weight residual 1.293 1.428 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C3' AAB I -30 " pdb=" O3' AAB I -30 " ideal model delta sigma weight residual 1.362 1.431 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4' AAB I -30 " pdb=" C3' AAB I -30 " ideal model delta sigma weight residual 1.576 1.518 0.058 2.00e-02 2.50e+03 8.40e+00 ... (remaining 13729 not shown) Histogram of bond angle deviations from ideal: 95.91 - 103.83: 833 103.83 - 111.75: 7138 111.75 - 119.67: 5408 119.67 - 127.60: 5872 127.60 - 135.52: 422 Bond angle restraints: 19673 Sorted by residual: angle pdb=" N GLU H 110 " pdb=" CA GLU H 110 " pdb=" CB GLU H 110 " ideal model delta sigma weight residual 110.39 116.95 -6.56 1.66e+00 3.63e-01 1.56e+01 angle pdb=" C ASP K 239 " pdb=" CA ASP K 239 " pdb=" CB ASP K 239 " ideal model delta sigma weight residual 116.63 112.56 4.07 1.16e+00 7.43e-01 1.23e+01 angle pdb=" O1P AAB I -30 " pdb=" P AAB I -30 " pdb=" O3P AAB I -30 " ideal model delta sigma weight residual 109.47 119.91 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CA VAL K 96 " pdb=" C VAL K 96 " pdb=" N PRO K 97 " ideal model delta sigma weight residual 118.88 124.23 -5.35 1.54e+00 4.22e-01 1.21e+01 angle pdb=" CG ARG E 49 " pdb=" CD ARG E 49 " pdb=" NE ARG E 49 " ideal model delta sigma weight residual 112.00 119.62 -7.62 2.20e+00 2.07e-01 1.20e+01 ... (remaining 19668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 6272 35.16 - 70.31: 1288 70.31 - 105.47: 21 105.47 - 140.62: 2 140.62 - 175.78: 1 Dihedral angle restraints: 7584 sinusoidal: 4826 harmonic: 2758 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.78 -175.78 1 3.50e+01 8.16e-04 1.57e+01 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 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP K 239 " pdb=" C ASP K 239 " pdb=" N GLU K 240 " pdb=" CA GLU K 240 " ideal model delta harmonic sigma weight residual 180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1872 0.058 - 0.116: 309 0.116 - 0.175: 41 0.175 - 0.233: 3 0.233 - 0.291: 4 Chirality restraints: 2229 Sorted by residual: chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA GLU H 110 " pdb=" N GLU H 110 " pdb=" C GLU H 110 " pdb=" CB GLU H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2226 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP K 243 " 0.022 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP K 243 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP K 243 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP K 243 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 243 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP K 243 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 243 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 243 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 243 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP K 243 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO G 80 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO C 80 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.035 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2879 2.81 - 3.33: 10403 3.33 - 3.85: 25077 3.85 - 4.38: 29267 4.38 - 4.90: 42803 Nonbonded interactions: 110429 Sorted by model distance: nonbonded pdb=" O GLN K 93 " pdb=" OG SER K 172 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.336 2.440 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.344 2.440 nonbonded pdb=" NH2 ARG K 234 " pdb=" O GLN K 238 " model vdw 2.376 2.520 ... (remaining 110424 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 121) selection = chain 'H' } 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: 0.380 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: 2.460 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 41.620 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.006 0.180 13734 Z= 0.302 Angle : 0.767 10.516 19673 Z= 0.435 Chirality : 0.045 0.291 2229 Planarity : 0.007 0.073 1591 Dihedral : 26.282 175.776 5808 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.59 (0.23), residues: 935 helix: -0.54 (0.18), residues: 571 sheet: -1.91 (0.62), residues: 49 loop : -1.66 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP K 243 HIS 0.005 0.001 HIS F 75 PHE 0.034 0.002 PHE C 25 TYR 0.041 0.003 TYR F 98 ARG 0.015 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7866 (mt-10) REVERT: B 77 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7830 (mttp) REVERT: B 79 LYS cc_start: 0.8263 (mmtp) cc_final: 0.7837 (mmtt) REVERT: C 62 ILE cc_start: 0.8281 (mm) cc_final: 0.8058 (mt) REVERT: D 64 ASN cc_start: 0.8467 (m-40) cc_final: 0.8133 (m-40) REVERT: H 59 MET cc_start: 0.8602 (mmm) cc_final: 0.8150 (mmm) REVERT: H 83 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7391 (mmt90) REVERT: K 108 VAL cc_start: 0.4155 (t) cc_final: 0.3406 (m) REVERT: K 120 ARG cc_start: 0.3511 (tmm160) cc_final: 0.2952 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.9482 time to fit residues: 339.7788 Evaluate side-chains 104 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 94 ASN D 79 HIS E 76 GLN F 27 GLN G 68 ASN G 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13734 Z= 0.321 Angle : 0.618 8.312 19673 Z= 0.357 Chirality : 0.040 0.193 2229 Planarity : 0.006 0.055 1591 Dihedral : 29.938 175.214 3937 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.77 % Allowed : 12.66 % Favored : 85.57 % 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: -0.45 (0.26), residues: 935 helix: 0.53 (0.21), residues: 581 sheet: -1.73 (0.66), residues: 47 loop : -1.58 (0.29), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP K 243 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.002 PHE D 67 TYR 0.024 0.003 TYR F 98 ARG 0.009 0.001 ARG K 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.828 Fit side-chains REVERT: B 63 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 77 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7832 (mttp) REVERT: B 79 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7984 (mmtt) REVERT: C 15 LYS cc_start: 0.7307 (tttp) cc_final: 0.6961 (ttpp) REVERT: C 62 ILE cc_start: 0.8452 (mm) cc_final: 0.8182 (mt) REVERT: D 43 LYS cc_start: 0.8310 (mmpt) cc_final: 0.8022 (mmpt) REVERT: D 119 THR cc_start: 0.8192 (p) cc_final: 0.7986 (m) REVERT: E 68 GLN cc_start: 0.8229 (tt0) cc_final: 0.7937 (tt0) REVERT: F 52 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7245 (tp30) REVERT: G 77 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7177 (mtp180) REVERT: H 83 ARG cc_start: 0.7634 (mmt-90) cc_final: 0.7190 (mmt90) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 1.7630 time to fit residues: 234.5703 Evaluate side-chains 107 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 60 ASN E 125 GLN F 27 GLN G 73 ASN G 104 GLN H 60 ASN H 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13734 Z= 0.357 Angle : 0.635 7.683 19673 Z= 0.367 Chirality : 0.041 0.187 2229 Planarity : 0.006 0.050 1591 Dihedral : 30.119 175.156 3937 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.78 % Allowed : 13.04 % Favored : 84.18 % 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 (0.26), residues: 935 helix: 0.68 (0.21), residues: 583 sheet: -1.76 (0.64), residues: 48 loop : -1.44 (0.30), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 243 HIS 0.006 0.001 HIS B 75 PHE 0.010 0.002 PHE D 67 TYR 0.018 0.002 TYR K 159 ARG 0.005 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.127 Fit side-chains REVERT: A 50 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7631 (mt-10) REVERT: B 77 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7904 (mttp) REVERT: C 15 LYS cc_start: 0.7102 (tttp) cc_final: 0.6862 (ttpp) REVERT: C 62 ILE cc_start: 0.8460 (mm) cc_final: 0.8195 (mt) REVERT: D 43 LYS cc_start: 0.8418 (mmpt) cc_final: 0.8099 (mmpt) REVERT: E 63 ARG cc_start: 0.8374 (mmp80) cc_final: 0.8119 (mmp80) REVERT: E 68 GLN cc_start: 0.8266 (tt0) cc_final: 0.8031 (tt0) REVERT: E 83 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7523 (mtt180) REVERT: G 77 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7310 (mtp180) REVERT: H 83 ARG cc_start: 0.7689 (mmt-90) cc_final: 0.7225 (mmt90) REVERT: H 105 LYS cc_start: 0.7968 (mttm) cc_final: 0.7694 (mttm) REVERT: K 187 LEU cc_start: 0.2771 (pp) cc_final: 0.2478 (mt) outliers start: 22 outliers final: 15 residues processed: 124 average time/residue: 1.7059 time to fit residues: 225.4647 Evaluate side-chains 120 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain K residue 164 MET Chi-restraints excluded: chain K residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 114 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN E 108 ASN F 27 GLN G 38 ASN G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13734 Z= 0.200 Angle : 0.572 8.522 19673 Z= 0.338 Chirality : 0.037 0.144 2229 Planarity : 0.005 0.050 1591 Dihedral : 30.053 175.898 3937 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.03 % Allowed : 15.06 % Favored : 82.91 % 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: 0.26 (0.27), residues: 935 helix: 1.17 (0.22), residues: 575 sheet: -1.89 (0.64), residues: 50 loop : -1.32 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 243 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE E 67 TYR 0.014 0.002 TYR K 159 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.037 Fit side-chains REVERT: A 50 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 77 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7920 (mttp) REVERT: C 15 LYS cc_start: 0.7085 (tttp) cc_final: 0.6850 (ttpp) REVERT: C 62 ILE cc_start: 0.8400 (mm) cc_final: 0.8116 (mt) REVERT: D 43 LYS cc_start: 0.8409 (mmpt) cc_final: 0.8108 (mmpt) REVERT: E 83 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7441 (mtt180) REVERT: G 77 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7287 (mtp180) REVERT: H 83 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7302 (mmt90) REVERT: H 105 LYS cc_start: 0.7902 (mttm) cc_final: 0.7654 (mttm) REVERT: K 187 LEU cc_start: 0.2753 (pp) cc_final: 0.2492 (mt) outliers start: 16 outliers final: 9 residues processed: 113 average time/residue: 1.7108 time to fit residues: 206.1910 Evaluate side-chains 109 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 164 MET 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 60 ASN F 27 GLN G 38 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13734 Z= 0.312 Angle : 0.601 7.536 19673 Z= 0.351 Chirality : 0.040 0.145 2229 Planarity : 0.005 0.047 1591 Dihedral : 30.045 175.373 3937 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.16 % Allowed : 15.06 % Favored : 81.77 % 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: 0.22 (0.26), residues: 935 helix: 1.11 (0.22), residues: 575 sheet: -1.99 (0.63), residues: 50 loop : -1.26 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 243 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.002 PHE A 104 TYR 0.017 0.002 TYR K 159 ARG 0.005 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.031 Fit side-chains REVERT: A 50 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 62 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8125 (mt) REVERT: D 39 TYR cc_start: 0.7396 (m-10) cc_final: 0.6867 (t80) REVERT: D 43 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8112 (mmpt) REVERT: E 68 GLN cc_start: 0.8257 (tt0) cc_final: 0.7973 (tt0) REVERT: E 83 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7506 (mtt180) REVERT: G 77 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7346 (mtp180) REVERT: H 83 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7385 (mmt90) REVERT: H 105 LYS cc_start: 0.7931 (mttm) cc_final: 0.7683 (mttm) REVERT: K 187 LEU cc_start: 0.2730 (pp) cc_final: 0.2457 (mt) outliers start: 25 outliers final: 16 residues processed: 119 average time/residue: 1.7224 time to fit residues: 218.6821 Evaluate side-chains 114 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 155 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 27 GLN G 38 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13734 Z= 0.280 Angle : 0.595 8.443 19673 Z= 0.347 Chirality : 0.038 0.143 2229 Planarity : 0.005 0.106 1591 Dihedral : 30.036 175.703 3937 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.78 % Allowed : 16.58 % Favored : 80.63 % 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: 0.31 (0.27), residues: 935 helix: 1.19 (0.22), residues: 574 sheet: -2.01 (0.63), residues: 50 loop : -1.24 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 243 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.002 PHE A 104 TYR 0.016 0.002 TYR K 159 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.126 Fit side-chains REVERT: A 50 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7618 (mt-10) REVERT: C 62 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8121 (mt) REVERT: D 39 TYR cc_start: 0.7321 (m-80) cc_final: 0.6858 (t80) REVERT: D 43 LYS cc_start: 0.8414 (mmpt) cc_final: 0.8117 (mmpt) REVERT: E 63 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7836 (mmt-90) REVERT: E 68 GLN cc_start: 0.8244 (tt0) cc_final: 0.7965 (tt0) REVERT: E 83 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7498 (mtt180) REVERT: G 77 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7336 (mtp180) REVERT: H 83 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7379 (mmt90) REVERT: H 105 LYS cc_start: 0.7933 (mttm) cc_final: 0.7690 (mttm) REVERT: K 187 LEU cc_start: 0.2726 (pp) cc_final: 0.2453 (mt) outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 1.7383 time to fit residues: 216.6604 Evaluate side-chains 119 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 155 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0070 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 27 GLN G 38 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13734 Z= 0.164 Angle : 0.564 7.363 19673 Z= 0.333 Chirality : 0.035 0.143 2229 Planarity : 0.005 0.074 1591 Dihedral : 30.026 176.275 3937 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.91 % Allowed : 16.96 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.27), residues: 935 helix: 1.44 (0.22), residues: 574 sheet: -1.96 (0.64), residues: 50 loop : -1.18 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 243 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.001 TYR F 51 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.127 Fit side-chains REVERT: A 50 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 77 LYS cc_start: 0.7985 (mttp) cc_final: 0.7687 (mttp) REVERT: C 62 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8094 (mt) REVERT: D 39 TYR cc_start: 0.7277 (m-80) cc_final: 0.6812 (t80) REVERT: D 43 LYS cc_start: 0.8406 (mmpt) cc_final: 0.8111 (mmpt) REVERT: E 63 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7819 (mmt-90) REVERT: E 83 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7442 (mtt180) REVERT: E 90 MET cc_start: 0.7863 (mmm) cc_final: 0.7578 (mmp) REVERT: H 83 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7350 (mmt90) REVERT: H 105 LYS cc_start: 0.7869 (mttm) cc_final: 0.7634 (mttm) REVERT: K 187 LEU cc_start: 0.2711 (pp) cc_final: 0.2448 (mt) outliers start: 23 outliers final: 17 residues processed: 114 average time/residue: 1.6632 time to fit residues: 202.6151 Evaluate side-chains 116 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 164 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 27 GLN G 38 ASN G 73 ASN G 104 GLN H 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13734 Z= 0.206 Angle : 0.562 7.370 19673 Z= 0.331 Chirality : 0.036 0.141 2229 Planarity : 0.004 0.057 1591 Dihedral : 29.980 175.928 3937 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.78 % Allowed : 17.47 % Favored : 79.75 % 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: 0.64 (0.27), residues: 935 helix: 1.45 (0.22), residues: 574 sheet: -1.82 (0.64), residues: 54 loop : -1.08 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 243 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.013 0.002 TYR K 159 ARG 0.006 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.046 Fit side-chains REVERT: B 77 LYS cc_start: 0.8001 (mttp) cc_final: 0.7701 (mttp) REVERT: C 62 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8074 (mt) REVERT: D 39 TYR cc_start: 0.7229 (m-80) cc_final: 0.6749 (t80) REVERT: D 43 LYS cc_start: 0.8418 (mmpt) cc_final: 0.8125 (mmpt) REVERT: E 63 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7723 (mmt-90) REVERT: E 83 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7482 (mtt180) REVERT: G 77 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7325 (mtp180) REVERT: H 83 ARG cc_start: 0.7697 (mmt-90) cc_final: 0.7349 (mmt90) REVERT: H 105 LYS cc_start: 0.7936 (mttm) cc_final: 0.7703 (mttm) REVERT: K 187 LEU cc_start: 0.2703 (pp) cc_final: 0.2446 (mt) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 1.8145 time to fit residues: 224.9479 Evaluate side-chains 117 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 164 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 27 GLN G 38 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13734 Z= 0.347 Angle : 0.624 7.469 19673 Z= 0.362 Chirality : 0.041 0.146 2229 Planarity : 0.005 0.045 1591 Dihedral : 30.095 174.804 3937 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.91 % Allowed : 17.85 % Favored : 79.24 % 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: 0.28 (0.27), residues: 935 helix: 1.12 (0.22), residues: 575 sheet: -1.98 (0.63), residues: 54 loop : -1.12 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 243 HIS 0.005 0.001 HIS B 75 PHE 0.010 0.002 PHE A 104 TYR 0.017 0.002 TYR K 159 ARG 0.005 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.082 Fit side-chains REVERT: A 50 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7649 (mt-10) REVERT: C 62 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8144 (mt) REVERT: D 39 TYR cc_start: 0.7293 (m-80) cc_final: 0.6818 (t80) REVERT: D 43 LYS cc_start: 0.8430 (mmpt) cc_final: 0.8124 (mmpt) REVERT: E 68 GLN cc_start: 0.8269 (tt0) cc_final: 0.8065 (tt0) REVERT: E 83 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7526 (mtt180) REVERT: G 77 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7371 (mtp180) REVERT: H 59 MET cc_start: 0.8491 (mmm) cc_final: 0.8274 (mmm) REVERT: H 83 ARG cc_start: 0.7796 (mmt-90) cc_final: 0.7403 (mmt90) REVERT: H 105 LYS cc_start: 0.7950 (mttm) cc_final: 0.7695 (mttm) outliers start: 23 outliers final: 18 residues processed: 121 average time/residue: 1.7020 time to fit residues: 219.5368 Evaluate side-chains 122 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 164 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 0.0040 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13734 Z= 0.254 Angle : 0.599 7.572 19673 Z= 0.350 Chirality : 0.038 0.143 2229 Planarity : 0.005 0.046 1591 Dihedral : 30.098 175.439 3937 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.66 % Allowed : 18.99 % Favored : 78.35 % 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: 0.36 (0.27), residues: 935 helix: 1.18 (0.22), residues: 575 sheet: -1.95 (0.63), residues: 54 loop : -1.10 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 243 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.002 PHE A 104 TYR 0.015 0.002 TYR K 159 ARG 0.004 0.000 ARG B 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.050 Fit side-chains REVERT: C 62 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8125 (mt) REVERT: D 39 TYR cc_start: 0.7280 (m-80) cc_final: 0.6794 (t80) REVERT: D 43 LYS cc_start: 0.8425 (mmpt) cc_final: 0.8118 (mmpt) REVERT: E 68 GLN cc_start: 0.8243 (tt0) cc_final: 0.7973 (tt0) REVERT: E 83 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7473 (mtt180) REVERT: G 77 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7362 (mtp180) REVERT: H 83 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7382 (mmt90) REVERT: H 105 LYS cc_start: 0.7933 (mttm) cc_final: 0.7681 (mttm) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 1.7415 time to fit residues: 215.2265 Evaluate side-chains 119 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain K residue 164 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.180240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130394 restraints weight = 13683.145| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.17 r_work: 0.3099 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13734 Z= 0.222 Angle : 0.587 7.414 19673 Z= 0.345 Chirality : 0.037 0.143 2229 Planarity : 0.005 0.045 1591 Dihedral : 30.078 175.544 3937 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.91 % Allowed : 18.86 % Favored : 78.23 % 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: 0.40 (0.27), residues: 935 helix: 1.22 (0.22), residues: 575 sheet: -1.94 (0.63), residues: 54 loop : -1.09 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 243 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.014 0.002 TYR K 159 ARG 0.005 0.000 ARG K 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4220.61 seconds wall clock time: 75 minutes 6.70 seconds (4506.70 seconds total)