Starting phenix.real_space_refine on Wed Mar 4 15:23:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zni_11312/03_2026/6zni_11312.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zni_11312/03_2026/6zni_11312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zni_11312/03_2026/6zni_11312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zni_11312/03_2026/6zni_11312.map" model { file = "/net/cci-nas-00/data/ceres_data/6zni_11312/03_2026/6zni_11312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zni_11312/03_2026/6zni_11312.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 3 Type Number sf(0) Gaussians C 9246 2.51 5 N 2438 2.21 5 O 3128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14812 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W Time building chain proxies: 1.25, per 1000 atoms: 0.08 Number of scatterers: 14812 At special positions: 0 Unit cell: (84.4051, 84.4051, 171.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3128 8.00 N 2438 7.00 C 9246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 651.8 milliseconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 24 through 40 Processing helix chain 'A' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 24 through 40 Processing helix chain 'B' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 24 through 40 Processing helix chain 'D' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 24 through 40 Processing helix chain 'G' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 23 Processing helix chain 'H' and resid 24 through 40 Processing helix chain 'H' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 Processing helix chain 'I' and resid 24 through 40 Processing helix chain 'I' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN I 81 " --> pdb=" O ALA I 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 23 Processing helix chain 'J' and resid 24 through 40 Processing helix chain 'J' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 23 Processing helix chain 'K' and resid 24 through 40 Processing helix chain 'K' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 23 Processing helix chain 'L' and resid 24 through 40 Processing helix chain 'L' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 23 Processing helix chain 'M' and resid 24 through 40 Processing helix chain 'M' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 23 Processing helix chain 'N' and resid 24 through 40 Processing helix chain 'N' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 23 Processing helix chain 'O' and resid 24 through 40 Processing helix chain 'O' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 23 Processing helix chain 'P' and resid 24 through 40 Processing helix chain 'P' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 23 Processing helix chain 'Q' and resid 24 through 40 Processing helix chain 'Q' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN Q 81 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 23 Processing helix chain 'R' and resid 24 through 40 Processing helix chain 'R' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 23 Processing helix chain 'S' and resid 24 through 40 Processing helix chain 'S' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN S 81 " --> pdb=" O ALA S 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 23 Processing helix chain 'T' and resid 24 through 40 Processing helix chain 'T' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN T 81 " --> pdb=" O ALA T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 23 Processing helix chain 'U' and resid 24 through 40 Processing helix chain 'U' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN U 81 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 23 Processing helix chain 'V' and resid 24 through 40 Processing helix chain 'V' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN V 81 " --> pdb=" O ALA V 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 23 Processing helix chain 'W' and resid 24 through 40 Processing helix chain 'W' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2691 1.29 - 1.35: 2277 1.35 - 1.41: 1064 1.41 - 1.48: 2363 1.48 - 1.54: 6624 Bond restraints: 15019 Sorted by residual: bond pdb=" CA THR P 23 " pdb=" CB THR P 23 " ideal model delta sigma weight residual 1.539 1.482 0.058 4.88e-02 4.20e+02 1.39e+00 bond pdb=" CA THR R 23 " pdb=" CB THR R 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.39e+00 bond pdb=" CA THR U 23 " pdb=" CB THR U 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.37e+00 bond pdb=" CA THR B 23 " pdb=" CB THR B 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.37e+00 bond pdb=" CA THR S 23 " pdb=" CB THR S 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.37e+00 ... (remaining 15014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 18622 0.94 - 1.88: 1519 1.88 - 2.82: 158 2.82 - 3.76: 127 3.76 - 4.70: 44 Bond angle restraints: 20470 Sorted by residual: angle pdb=" N ASP D 8 " pdb=" CA ASP D 8 " pdb=" C ASP D 8 " ideal model delta sigma weight residual 111.75 115.40 -3.65 1.28e+00 6.10e-01 8.12e+00 angle pdb=" N ASP M 8 " pdb=" CA ASP M 8 " pdb=" C ASP M 8 " ideal model delta sigma weight residual 111.75 115.38 -3.63 1.28e+00 6.10e-01 8.06e+00 angle pdb=" N ASP S 8 " pdb=" CA ASP S 8 " pdb=" C ASP S 8 " ideal model delta sigma weight residual 111.75 115.38 -3.63 1.28e+00 6.10e-01 8.03e+00 angle pdb=" N ASP T 8 " pdb=" CA ASP T 8 " pdb=" C ASP T 8 " ideal model delta sigma weight residual 111.75 115.38 -3.63 1.28e+00 6.10e-01 8.03e+00 angle pdb=" N ASP E 8 " pdb=" CA ASP E 8 " pdb=" C ASP E 8 " ideal model delta sigma weight residual 111.75 115.37 -3.62 1.28e+00 6.10e-01 8.01e+00 ... (remaining 20465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 8627 17.14 - 34.27: 412 34.27 - 51.40: 161 51.40 - 68.54: 0 68.54 - 85.67: 23 Dihedral angle restraints: 9223 sinusoidal: 3611 harmonic: 5612 Sorted by residual: dihedral pdb=" CA ASP D 9 " pdb=" C ASP D 9 " pdb=" N TRP D 10 " pdb=" CA TRP D 10 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP B 9 " pdb=" C ASP B 9 " pdb=" N TRP B 10 " pdb=" CA TRP B 10 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP I 9 " pdb=" C ASP I 9 " pdb=" N TRP I 10 " pdb=" CA TRP I 10 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1138 0.025 - 0.049: 1022 0.049 - 0.074: 171 0.074 - 0.099: 38 0.099 - 0.124: 92 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA PRO P 44 " pdb=" N PRO P 44 " pdb=" C PRO P 44 " pdb=" CB PRO P 44 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA PRO S 44 " pdb=" N PRO S 44 " pdb=" C PRO S 44 " pdb=" CB PRO S 44 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO Q 44 " pdb=" N PRO Q 44 " pdb=" C PRO Q 44 " pdb=" CB PRO Q 44 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 2458 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 5 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO H 6 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 6 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 6 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 5 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO E 6 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 6 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 6 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 5 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 6 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 6 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 6 " 0.027 5.00e-02 4.00e+02 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 395 2.68 - 3.24: 16130 3.24 - 3.79: 25885 3.79 - 4.35: 28758 4.35 - 4.90: 51677 Nonbonded interactions: 122845 Sorted by model distance: nonbonded pdb=" ND2 ASN G 43 " pdb=" O ASP Q 8 " model vdw 2.130 3.120 nonbonded pdb=" OG SER R 65 " pdb=" ND2 ASN W 81 " model vdw 2.151 3.120 nonbonded pdb=" OG SER C 65 " pdb=" ND2 ASN O 81 " model vdw 2.183 3.120 nonbonded pdb=" OG SER M 65 " pdb=" ND2 ASN R 81 " model vdw 2.190 3.120 nonbonded pdb=" ND2 ASN E 43 " pdb=" O ASP S 8 " model vdw 2.197 3.120 ... (remaining 122840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.950 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 0.058 15019 Z= 0.325 Angle : 0.612 4.697 20470 Z= 0.368 Chirality : 0.038 0.124 2461 Planarity : 0.006 0.049 2668 Dihedral : 12.209 85.675 5543 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.70 % Allowed : 9.46 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1840 helix: 1.99 (0.12), residues: 1564 sheet: None (None), residues: 0 loop : -3.28 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG K 61 TYR 0.010 0.002 TYR M 60 PHE 0.005 0.001 PHE M 19 TRP 0.005 0.002 TRP H 10 Details of bonding type rmsd covalent geometry : bond 0.00732 (15019) covalent geometry : angle 0.61207 (20470) hydrogen bonds : bond 0.13048 ( 1288) hydrogen bonds : angle 5.31332 ( 3864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 1103 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8228 (t70) REVERT: A 39 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9203 (mmmt) REVERT: A 60 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8044 (t80) REVERT: A 79 ILE cc_start: 0.9196 (mm) cc_final: 0.8941 (mm) REVERT: B 50 TYR cc_start: 0.8949 (t80) cc_final: 0.8713 (t80) REVERT: C 23 THR cc_start: 0.9317 (m) cc_final: 0.9095 (p) REVERT: C 50 TYR cc_start: 0.9045 (t80) cc_final: 0.8231 (t80) REVERT: C 56 GLU cc_start: 0.8901 (tt0) cc_final: 0.8419 (mm-30) REVERT: C 60 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.7362 (t80) REVERT: D 29 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8236 (mt-10) REVERT: D 49 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8198 (mt-10) REVERT: D 50 TYR cc_start: 0.8989 (t80) cc_final: 0.8236 (t80) REVERT: D 56 GLU cc_start: 0.8948 (tt0) cc_final: 0.8714 (mt-10) REVERT: D 60 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8355 (t80) REVERT: E 25 THR cc_start: 0.8758 (t) cc_final: 0.8556 (t) REVERT: E 30 LEU cc_start: 0.9007 (tp) cc_final: 0.8777 (tp) REVERT: E 45 GLN cc_start: 0.8767 (tp40) cc_final: 0.8480 (tp40) REVERT: E 80 GLN cc_start: 0.8828 (tt0) cc_final: 0.8551 (tp-100) REVERT: F 24 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8717 (tp-100) REVERT: F 45 GLN cc_start: 0.8623 (tp40) cc_final: 0.7670 (tm-30) REVERT: F 49 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7191 (mt-10) REVERT: F 50 TYR cc_start: 0.9082 (t80) cc_final: 0.8852 (t80) REVERT: G 17 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8639 (mm-30) REVERT: G 21 ASP cc_start: 0.8804 (m-30) cc_final: 0.8543 (m-30) REVERT: G 24 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8268 (tp40) REVERT: G 27 GLN cc_start: 0.9088 (mt0) cc_final: 0.8187 (mt0) REVERT: G 45 GLN cc_start: 0.8901 (tp40) cc_final: 0.8436 (tm-30) REVERT: G 49 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7803 (mt-10) REVERT: G 72 LYS cc_start: 0.8750 (ttpt) cc_final: 0.8038 (ttmt) REVERT: H 16 SER cc_start: 0.8726 (m) cc_final: 0.8233 (m) REVERT: H 23 THR cc_start: 0.8850 (m) cc_final: 0.8574 (p) REVERT: H 42 SER cc_start: 0.9014 (p) cc_final: 0.8762 (m) REVERT: H 56 GLU cc_start: 0.9028 (tt0) cc_final: 0.8749 (mm-30) REVERT: H 69 LYS cc_start: 0.8531 (tptp) cc_final: 0.8321 (tptp) REVERT: H 72 LYS cc_start: 0.8661 (ttpt) cc_final: 0.7917 (ttmt) REVERT: I 20 ASP cc_start: 0.8895 (m-30) cc_final: 0.8663 (m-30) REVERT: I 23 THR cc_start: 0.9363 (m) cc_final: 0.9038 (p) REVERT: I 45 GLN cc_start: 0.8973 (tp40) cc_final: 0.8771 (tp40) REVERT: I 56 GLU cc_start: 0.9036 (tt0) cc_final: 0.8608 (mt-10) REVERT: I 60 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8531 (t80) REVERT: I 72 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8081 (ttmt) REVERT: J 50 TYR cc_start: 0.8996 (t80) cc_final: 0.8487 (t80) REVERT: J 56 GLU cc_start: 0.9032 (tt0) cc_final: 0.8687 (mt-10) REVERT: J 72 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8039 (ttmt) REVERT: J 80 GLN cc_start: 0.8841 (tt0) cc_final: 0.8527 (tp-100) REVERT: K 8 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8296 (t70) REVERT: K 21 ASP cc_start: 0.8770 (m-30) cc_final: 0.8349 (m-30) REVERT: K 56 GLU cc_start: 0.9023 (tt0) cc_final: 0.8606 (mt-10) REVERT: K 60 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8197 (t80) REVERT: K 72 LYS cc_start: 0.8900 (ttpt) cc_final: 0.7990 (ttmt) REVERT: L 8 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8262 (t70) REVERT: L 24 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8842 (tp40) REVERT: L 45 GLN cc_start: 0.8578 (tp40) cc_final: 0.7943 (tm-30) REVERT: L 56 GLU cc_start: 0.9169 (tt0) cc_final: 0.8663 (mt-10) REVERT: L 60 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8229 (t80) REVERT: L 72 LYS cc_start: 0.8582 (ttpt) cc_final: 0.7864 (ttmt) REVERT: N 8 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8429 (t70) REVERT: N 20 ASP cc_start: 0.9211 (m-30) cc_final: 0.8987 (m-30) REVERT: N 21 ASP cc_start: 0.8810 (m-30) cc_final: 0.8071 (m-30) REVERT: N 27 GLN cc_start: 0.8970 (mt0) cc_final: 0.8442 (mp10) REVERT: N 42 SER cc_start: 0.8789 (p) cc_final: 0.8362 (p) REVERT: N 45 GLN cc_start: 0.8564 (tp40) cc_final: 0.8300 (tp40) REVERT: N 49 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7637 (mt-10) REVERT: O 8 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8476 (t70) REVERT: O 21 ASP cc_start: 0.8641 (m-30) cc_final: 0.8239 (m-30) REVERT: O 29 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8387 (mt-10) REVERT: O 42 SER cc_start: 0.9050 (p) cc_final: 0.8587 (p) REVERT: O 45 GLN cc_start: 0.8621 (tp40) cc_final: 0.7755 (tm-30) REVERT: O 49 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7414 (mt-10) REVERT: O 80 GLN cc_start: 0.9123 (tt0) cc_final: 0.8816 (tp40) REVERT: Q 45 GLN cc_start: 0.8627 (tp40) cc_final: 0.8224 (tm-30) REVERT: Q 49 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7135 (mt-10) REVERT: R 20 ASP cc_start: 0.9081 (m-30) cc_final: 0.8787 (m-30) REVERT: R 60 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8212 (t80) REVERT: R 80 GLN cc_start: 0.8711 (tt0) cc_final: 0.8401 (tp-100) REVERT: S 14 SER cc_start: 0.9129 (t) cc_final: 0.8875 (p) REVERT: S 20 ASP cc_start: 0.9170 (m-30) cc_final: 0.8911 (m-30) REVERT: S 21 ASP cc_start: 0.8632 (m-30) cc_final: 0.8364 (m-30) REVERT: S 46 LEU cc_start: 0.9432 (tp) cc_final: 0.9183 (tt) REVERT: S 56 GLU cc_start: 0.8678 (tt0) cc_final: 0.8393 (mm-30) REVERT: S 60 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8491 (t80) REVERT: S 69 LYS cc_start: 0.8394 (tptp) cc_final: 0.7887 (ttmt) REVERT: S 79 ILE cc_start: 0.9128 (mm) cc_final: 0.8820 (mm) REVERT: S 80 GLN cc_start: 0.8968 (tt0) cc_final: 0.8587 (tp-100) REVERT: T 21 ASP cc_start: 0.8796 (m-30) cc_final: 0.8379 (m-30) REVERT: T 56 GLU cc_start: 0.8852 (tt0) cc_final: 0.8297 (mm-30) REVERT: T 60 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7904 (t80) REVERT: T 69 LYS cc_start: 0.8352 (tptp) cc_final: 0.7880 (tppt) REVERT: U 20 ASP cc_start: 0.9091 (m-30) cc_final: 0.8864 (m-30) REVERT: U 23 THR cc_start: 0.9296 (m) cc_final: 0.8831 (p) REVERT: U 27 GLN cc_start: 0.8758 (mt0) cc_final: 0.8015 (tm-30) REVERT: U 56 GLU cc_start: 0.8886 (tt0) cc_final: 0.8200 (mm-30) REVERT: U 60 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8456 (t80) REVERT: U 69 LYS cc_start: 0.8032 (tptp) cc_final: 0.7677 (tppt) REVERT: V 20 ASP cc_start: 0.9032 (m-30) cc_final: 0.8792 (m-30) REVERT: V 39 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9181 (mmmm) REVERT: V 60 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8281 (t80) REVERT: V 69 LYS cc_start: 0.8217 (tptp) cc_final: 0.7914 (ttmt) REVERT: W 8 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8271 (t70) REVERT: W 16 SER cc_start: 0.8622 (m) cc_final: 0.7829 (m) REVERT: W 17 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8379 (mm-30) REVERT: W 20 ASP cc_start: 0.9191 (m-30) cc_final: 0.8836 (m-30) REVERT: W 21 ASP cc_start: 0.8824 (m-30) cc_final: 0.7591 (m-30) REVERT: W 29 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8399 (mt-10) REVERT: W 45 GLN cc_start: 0.8324 (tp40) cc_final: 0.8081 (tm-30) REVERT: W 69 LYS cc_start: 0.8194 (tptp) cc_final: 0.7853 (ttmt) REVERT: W 80 GLN cc_start: 0.8804 (tt0) cc_final: 0.8540 (tp40) outliers start: 46 outliers final: 12 residues processed: 1147 average time/residue: 0.0977 time to fit residues: 173.8276 Evaluate side-chains 986 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 957 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 27 GLN C 27 GLN D 27 GLN E 27 GLN E 64 GLN G 27 GLN H 27 GLN J 51 GLN K 27 GLN L 27 GLN M 27 GLN N 27 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN O 40 ASN P 27 GLN P 80 GLN Q 27 GLN R 27 GLN S 27 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 GLN U 27 GLN V 27 GLN W 27 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079859 restraints weight = 26483.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083341 restraints weight = 12772.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.085560 restraints weight = 7644.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087408 restraints weight = 5410.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088818 restraints weight = 4038.800| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15019 Z= 0.156 Angle : 0.659 9.859 20470 Z= 0.340 Chirality : 0.039 0.172 2461 Planarity : 0.007 0.054 2668 Dihedral : 6.899 51.510 2059 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.47 % Allowed : 23.38 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.30 (0.19), residues: 1840 helix: 3.60 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.90 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 61 TYR 0.014 0.001 TYR W 57 PHE 0.008 0.001 PHE D 19 TRP 0.010 0.002 TRP N 10 Details of bonding type rmsd covalent geometry : bond 0.00357 (15019) covalent geometry : angle 0.65860 (20470) hydrogen bonds : bond 0.05412 ( 1288) hydrogen bonds : angle 3.77233 ( 3864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1006 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 18 THR cc_start: 0.9186 (m) cc_final: 0.8843 (m) REVERT: A 56 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8393 (mm-30) REVERT: A 60 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8115 (t80) REVERT: B 49 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8281 (mt-10) REVERT: B 50 TYR cc_start: 0.8796 (t80) cc_final: 0.8285 (t80) REVERT: B 59 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9246 (mt) REVERT: C 21 ASP cc_start: 0.8507 (m-30) cc_final: 0.8032 (m-30) REVERT: C 23 THR cc_start: 0.9219 (m) cc_final: 0.8858 (p) REVERT: C 29 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8161 (mt-10) REVERT: C 56 GLU cc_start: 0.8972 (tt0) cc_final: 0.8501 (mm-30) REVERT: C 60 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7525 (t80) REVERT: D 24 GLN cc_start: 0.8507 (pm20) cc_final: 0.8303 (pm20) REVERT: D 49 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8310 (mt-10) REVERT: D 50 TYR cc_start: 0.8939 (t80) cc_final: 0.8392 (t80) REVERT: D 54 LEU cc_start: 0.8831 (tt) cc_final: 0.8571 (tt) REVERT: D 80 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8509 (tp-100) REVERT: E 45 GLN cc_start: 0.8646 (tp40) cc_final: 0.8255 (tp40) REVERT: E 56 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8693 (mt-10) REVERT: F 45 GLN cc_start: 0.8625 (tp40) cc_final: 0.7858 (tm-30) REVERT: F 49 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7512 (mt-10) REVERT: G 21 ASP cc_start: 0.8683 (m-30) cc_final: 0.8080 (m-30) REVERT: G 27 GLN cc_start: 0.9104 (mt0) cc_final: 0.8807 (mt0) REVERT: G 45 GLN cc_start: 0.8658 (tp40) cc_final: 0.8062 (tm-30) REVERT: G 49 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7477 (mt-10) REVERT: G 56 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8299 (mm-30) REVERT: G 72 LYS cc_start: 0.8861 (ttpt) cc_final: 0.7769 (tttt) REVERT: G 80 GLN cc_start: 0.8885 (tt0) cc_final: 0.8648 (tp-100) REVERT: H 20 ASP cc_start: 0.8818 (m-30) cc_final: 0.8497 (m-30) REVERT: H 23 THR cc_start: 0.9359 (m) cc_final: 0.8971 (p) REVERT: H 24 GLN cc_start: 0.8015 (pm20) cc_final: 0.7703 (pm20) REVERT: H 72 LYS cc_start: 0.8731 (ttpt) cc_final: 0.7927 (ttmt) REVERT: I 23 THR cc_start: 0.9320 (m) cc_final: 0.8973 (p) REVERT: I 27 GLN cc_start: 0.9067 (mt0) cc_final: 0.8361 (mt0) REVERT: I 42 SER cc_start: 0.8906 (p) cc_final: 0.7988 (p) REVERT: I 60 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8092 (t80) REVERT: I 72 LYS cc_start: 0.8897 (ttpt) cc_final: 0.7936 (ttmt) REVERT: J 18 THR cc_start: 0.9034 (m) cc_final: 0.8528 (m) REVERT: J 45 GLN cc_start: 0.8845 (tp40) cc_final: 0.8458 (tm-30) REVERT: J 72 LYS cc_start: 0.8936 (ttpt) cc_final: 0.7949 (ttmt) REVERT: K 21 ASP cc_start: 0.8657 (m-30) cc_final: 0.8255 (m-30) REVERT: K 56 GLU cc_start: 0.8930 (tt0) cc_final: 0.8642 (mt-10) REVERT: K 60 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.7749 (t80) REVERT: K 72 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8035 (ttmt) REVERT: L 45 GLN cc_start: 0.8345 (tp40) cc_final: 0.8044 (tm-30) REVERT: L 49 GLU cc_start: 0.8370 (mt-10) cc_final: 0.6953 (mt-10) REVERT: L 55 SER cc_start: 0.8686 (m) cc_final: 0.8374 (p) REVERT: L 56 GLU cc_start: 0.9123 (tt0) cc_final: 0.8833 (mt-10) REVERT: L 60 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7789 (t80) REVERT: L 72 LYS cc_start: 0.8730 (ttpt) cc_final: 0.7825 (ttmt) REVERT: M 21 ASP cc_start: 0.8800 (m-30) cc_final: 0.8279 (m-30) REVERT: M 23 THR cc_start: 0.8976 (p) cc_final: 0.8710 (p) REVERT: M 27 GLN cc_start: 0.9153 (mt0) cc_final: 0.8287 (mp10) REVERT: M 56 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8563 (mm-30) REVERT: N 20 ASP cc_start: 0.8942 (m-30) cc_final: 0.8679 (m-30) REVERT: N 21 ASP cc_start: 0.8561 (m-30) cc_final: 0.7703 (m-30) REVERT: N 24 GLN cc_start: 0.8442 (pm20) cc_final: 0.8158 (pm20) REVERT: N 27 GLN cc_start: 0.9094 (mt0) cc_final: 0.8434 (mt0) REVERT: N 42 SER cc_start: 0.8843 (p) cc_final: 0.8365 (p) REVERT: N 56 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8318 (mm-30) REVERT: N 80 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8469 (tp-100) REVERT: O 21 ASP cc_start: 0.8422 (m-30) cc_final: 0.7451 (m-30) REVERT: O 23 THR cc_start: 0.9318 (m) cc_final: 0.8846 (p) REVERT: O 24 GLN cc_start: 0.8232 (pm20) cc_final: 0.7994 (pm20) REVERT: O 45 GLN cc_start: 0.8630 (tp40) cc_final: 0.7822 (tm-30) REVERT: O 49 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7073 (mt-10) REVERT: O 56 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8535 (mm-30) REVERT: O 80 GLN cc_start: 0.8924 (tt0) cc_final: 0.8609 (tp-100) REVERT: P 21 ASP cc_start: 0.8509 (m-30) cc_final: 0.8185 (m-30) REVERT: P 56 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8236 (mm-30) REVERT: P 80 GLN cc_start: 0.8956 (tp40) cc_final: 0.8746 (tp40) REVERT: Q 45 GLN cc_start: 0.8552 (tp40) cc_final: 0.8161 (tm-30) REVERT: Q 49 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7073 (mt-10) REVERT: Q 56 GLU cc_start: 0.8880 (tt0) cc_final: 0.8566 (mt-10) REVERT: R 45 GLN cc_start: 0.8471 (tp40) cc_final: 0.7841 (tp40) REVERT: R 56 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6260 (mt-10) REVERT: R 60 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8177 (t80) REVERT: S 56 GLU cc_start: 0.8724 (tt0) cc_final: 0.8356 (mm-30) REVERT: S 62 ASN cc_start: 0.9206 (m-40) cc_final: 0.8933 (m-40) REVERT: S 69 LYS cc_start: 0.8858 (tptp) cc_final: 0.7410 (mttm) REVERT: S 79 ILE cc_start: 0.9123 (mm) cc_final: 0.8836 (mm) REVERT: T 18 THR cc_start: 0.8856 (m) cc_final: 0.8467 (m) REVERT: T 21 ASP cc_start: 0.8677 (m-30) cc_final: 0.8430 (m-30) REVERT: T 60 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7650 (t80) REVERT: T 69 LYS cc_start: 0.8700 (tptp) cc_final: 0.7960 (ttmt) REVERT: U 23 THR cc_start: 0.9236 (m) cc_final: 0.8582 (p) REVERT: U 27 GLN cc_start: 0.8899 (mt0) cc_final: 0.8141 (tm-30) REVERT: U 55 SER cc_start: 0.8934 (m) cc_final: 0.8679 (m) REVERT: U 56 GLU cc_start: 0.8964 (tt0) cc_final: 0.8602 (mm-30) REVERT: U 69 LYS cc_start: 0.8687 (tptp) cc_final: 0.7350 (mttm) REVERT: U 80 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8647 (tp-100) REVERT: V 21 ASP cc_start: 0.8719 (m-30) cc_final: 0.8181 (m-30) REVERT: V 24 GLN cc_start: 0.8274 (pm20) cc_final: 0.8012 (pm20) REVERT: V 39 LYS cc_start: 0.9333 (mmmt) cc_final: 0.9105 (mmmm) REVERT: V 60 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8217 (t80) REVERT: V 69 LYS cc_start: 0.8580 (tptp) cc_final: 0.7518 (mttm) REVERT: W 16 SER cc_start: 0.8633 (m) cc_final: 0.7970 (m) REVERT: W 20 ASP cc_start: 0.8968 (m-30) cc_final: 0.8749 (m-30) REVERT: W 21 ASP cc_start: 0.8567 (m-30) cc_final: 0.7937 (m-30) REVERT: W 23 THR cc_start: 0.9371 (m) cc_final: 0.9119 (p) REVERT: W 24 GLN cc_start: 0.8068 (pm20) cc_final: 0.7667 (pm20) REVERT: W 69 LYS cc_start: 0.8604 (tptp) cc_final: 0.7984 (ttmt) REVERT: W 80 GLN cc_start: 0.8870 (tt0) cc_final: 0.8477 (tp-100) outliers start: 76 outliers final: 48 residues processed: 1039 average time/residue: 0.0985 time to fit residues: 158.7468 Evaluate side-chains 1023 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 966 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 85 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 GLN G 40 ASN G 51 GLN I 27 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078747 restraints weight = 27399.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082189 restraints weight = 13395.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084572 restraints weight = 8091.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086354 restraints weight = 5621.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087660 restraints weight = 4231.212| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15019 Z= 0.166 Angle : 0.677 10.026 20470 Z= 0.347 Chirality : 0.038 0.195 2461 Planarity : 0.006 0.049 2668 Dihedral : 6.620 51.614 2047 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.99 % Allowed : 26.67 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.74 (0.19), residues: 1840 helix: 3.97 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -3.32 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 61 TYR 0.018 0.002 TYR J 50 PHE 0.006 0.001 PHE D 19 TRP 0.006 0.002 TRP M 10 Details of bonding type rmsd covalent geometry : bond 0.00381 (15019) covalent geometry : angle 0.67684 (20470) hydrogen bonds : bond 0.05162 ( 1288) hydrogen bonds : angle 3.70914 ( 3864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 969 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9315 (mmmt) cc_final: 0.8969 (mmmm) REVERT: A 56 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8386 (mm-30) REVERT: A 60 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8162 (t80) REVERT: A 79 ILE cc_start: 0.9086 (mm) cc_final: 0.8833 (mm) REVERT: B 49 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8388 (mt-10) REVERT: C 21 ASP cc_start: 0.8566 (m-30) cc_final: 0.8186 (m-30) REVERT: C 23 THR cc_start: 0.9248 (m) cc_final: 0.8980 (p) REVERT: C 39 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9202 (mmmt) REVERT: C 40 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8235 (p0) REVERT: C 56 GLU cc_start: 0.8834 (tt0) cc_final: 0.8545 (mm-30) REVERT: C 60 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.7658 (t80) REVERT: D 50 TYR cc_start: 0.8947 (t80) cc_final: 0.8568 (t80) REVERT: D 80 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8676 (tp-100) REVERT: E 27 GLN cc_start: 0.9052 (mt0) cc_final: 0.8774 (mt0) REVERT: E 45 GLN cc_start: 0.8524 (tp40) cc_final: 0.8274 (tp40) REVERT: E 64 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: F 24 GLN cc_start: 0.7883 (pm20) cc_final: 0.7558 (pm20) REVERT: F 45 GLN cc_start: 0.8660 (tp40) cc_final: 0.7834 (tm-30) REVERT: F 49 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7584 (mt-10) REVERT: G 21 ASP cc_start: 0.8520 (m-30) cc_final: 0.7906 (m-30) REVERT: G 24 GLN cc_start: 0.8399 (pm20) cc_final: 0.7986 (pm20) REVERT: G 45 GLN cc_start: 0.8708 (tp40) cc_final: 0.8091 (tm-30) REVERT: G 49 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7494 (mt-10) REVERT: G 56 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8322 (mm-30) REVERT: G 72 LYS cc_start: 0.8941 (ttpt) cc_final: 0.7685 (tttt) REVERT: H 20 ASP cc_start: 0.8879 (m-30) cc_final: 0.8603 (m-30) REVERT: H 23 THR cc_start: 0.9361 (m) cc_final: 0.9018 (p) REVERT: H 24 GLN cc_start: 0.8199 (pm20) cc_final: 0.7994 (pm20) REVERT: H 56 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8676 (mm-30) REVERT: H 72 LYS cc_start: 0.8861 (ttpt) cc_final: 0.7959 (ttmt) REVERT: I 20 ASP cc_start: 0.8917 (m-30) cc_final: 0.8537 (m-30) REVERT: I 23 THR cc_start: 0.9240 (m) cc_final: 0.9029 (p) REVERT: I 27 GLN cc_start: 0.9103 (mt0) cc_final: 0.8852 (mt0) REVERT: I 56 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8519 (mm-30) REVERT: I 60 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8151 (t80) REVERT: I 72 LYS cc_start: 0.8942 (ttpt) cc_final: 0.7965 (ttmt) REVERT: J 50 TYR cc_start: 0.9052 (t80) cc_final: 0.8678 (t80) REVERT: J 72 LYS cc_start: 0.8953 (ttpt) cc_final: 0.7935 (ttmt) REVERT: J 80 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8503 (tp-100) REVERT: K 21 ASP cc_start: 0.8570 (m-30) cc_final: 0.8238 (m-30) REVERT: K 56 GLU cc_start: 0.8950 (tt0) cc_final: 0.8597 (mt-10) REVERT: K 60 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7722 (t80) REVERT: K 72 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8009 (ttmt) REVERT: L 8 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8179 (t70) REVERT: L 40 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8281 (p0) REVERT: L 45 GLN cc_start: 0.8300 (tp40) cc_final: 0.7701 (tm-30) REVERT: L 49 GLU cc_start: 0.8407 (mt-10) cc_final: 0.6969 (mt-10) REVERT: L 56 GLU cc_start: 0.9147 (tt0) cc_final: 0.8884 (mt-10) REVERT: L 60 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7840 (t80) REVERT: L 72 LYS cc_start: 0.8755 (ttpt) cc_final: 0.7836 (ttmt) REVERT: M 21 ASP cc_start: 0.8592 (m-30) cc_final: 0.8167 (m-30) REVERT: M 24 GLN cc_start: 0.8264 (pm20) cc_final: 0.8026 (pm20) REVERT: M 32 LEU cc_start: 0.9424 (mm) cc_final: 0.8897 (mm) REVERT: M 42 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8610 (m) REVERT: M 56 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8570 (mm-30) REVERT: M 80 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8823 (tp-100) REVERT: N 20 ASP cc_start: 0.8972 (m-30) cc_final: 0.8656 (m-30) REVERT: N 21 ASP cc_start: 0.8658 (m-30) cc_final: 0.7888 (m-30) REVERT: N 24 GLN cc_start: 0.8717 (pm20) cc_final: 0.8370 (pm20) REVERT: N 27 GLN cc_start: 0.9017 (mt0) cc_final: 0.8413 (mt0) REVERT: N 42 SER cc_start: 0.8803 (p) cc_final: 0.8107 (m) REVERT: N 45 GLN cc_start: 0.8791 (tp40) cc_final: 0.8265 (tm-30) REVERT: N 56 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8191 (mm-30) REVERT: O 21 ASP cc_start: 0.8436 (m-30) cc_final: 0.7536 (m-30) REVERT: O 23 THR cc_start: 0.9266 (m) cc_final: 0.8799 (p) REVERT: O 24 GLN cc_start: 0.8487 (pm20) cc_final: 0.8182 (pm20) REVERT: O 27 GLN cc_start: 0.9059 (mt0) cc_final: 0.8654 (mt0) REVERT: O 45 GLN cc_start: 0.8598 (tp40) cc_final: 0.7938 (tm-30) REVERT: O 49 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7567 (mt-10) REVERT: O 56 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8454 (mm-30) REVERT: O 80 GLN cc_start: 0.8898 (tt0) cc_final: 0.8658 (tp-100) REVERT: P 24 GLN cc_start: 0.8068 (pm20) cc_final: 0.7709 (pm20) REVERT: P 35 ASP cc_start: 0.8933 (m-30) cc_final: 0.8685 (p0) REVERT: P 56 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8156 (mm-30) REVERT: P 80 GLN cc_start: 0.9067 (tp40) cc_final: 0.8823 (tp40) REVERT: Q 24 GLN cc_start: 0.7837 (pm20) cc_final: 0.7621 (pm20) REVERT: Q 35 ASP cc_start: 0.8741 (m-30) cc_final: 0.8503 (p0) REVERT: Q 45 GLN cc_start: 0.8361 (tp40) cc_final: 0.8061 (tm-30) REVERT: Q 49 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7061 (mt-10) REVERT: R 29 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8087 (mt-10) REVERT: R 45 GLN cc_start: 0.8537 (tp40) cc_final: 0.7853 (tp40) REVERT: R 56 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6214 (mt-10) REVERT: R 60 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8532 (t80) REVERT: S 56 GLU cc_start: 0.8835 (tt0) cc_final: 0.8179 (mm-30) REVERT: S 69 LYS cc_start: 0.8639 (tptp) cc_final: 0.7466 (mttm) REVERT: S 79 ILE cc_start: 0.9134 (mm) cc_final: 0.8875 (mm) REVERT: T 27 GLN cc_start: 0.8538 (mt0) cc_final: 0.7911 (tm-30) REVERT: T 30 LEU cc_start: 0.9036 (tp) cc_final: 0.8791 (tp) REVERT: T 60 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.7513 (t80) REVERT: T 69 LYS cc_start: 0.8585 (tptp) cc_final: 0.7538 (mttt) REVERT: U 23 THR cc_start: 0.9238 (m) cc_final: 0.8692 (p) REVERT: U 27 GLN cc_start: 0.8690 (mt0) cc_final: 0.8344 (tt0) REVERT: U 55 SER cc_start: 0.8943 (m) cc_final: 0.8715 (m) REVERT: U 56 GLU cc_start: 0.8986 (tt0) cc_final: 0.8436 (mm-30) REVERT: U 69 LYS cc_start: 0.8678 (tptp) cc_final: 0.7432 (mttm) REVERT: V 21 ASP cc_start: 0.8697 (m-30) cc_final: 0.8224 (m-30) REVERT: V 39 LYS cc_start: 0.9292 (mmmt) cc_final: 0.9087 (mmmm) REVERT: V 60 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8390 (t80) REVERT: V 69 LYS cc_start: 0.8571 (tptp) cc_final: 0.7365 (mttm) REVERT: V 80 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8737 (tp-100) REVERT: W 16 SER cc_start: 0.8726 (m) cc_final: 0.8104 (m) REVERT: W 21 ASP cc_start: 0.8576 (m-30) cc_final: 0.8002 (m-30) REVERT: W 23 THR cc_start: 0.9352 (m) cc_final: 0.9072 (p) REVERT: W 24 GLN cc_start: 0.8150 (pm20) cc_final: 0.7772 (pm20) REVERT: W 69 LYS cc_start: 0.8614 (tptp) cc_final: 0.8029 (ttmt) REVERT: W 80 GLN cc_start: 0.8831 (tt0) cc_final: 0.8592 (tp-100) outliers start: 102 outliers final: 65 residues processed: 1015 average time/residue: 0.0989 time to fit residues: 155.8756 Evaluate side-chains 1029 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 951 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 58 THR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 60 TYR Chi-restraints excluded: chain W residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 GLN F 40 ASN I 80 GLN K 80 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN S 80 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.078151 restraints weight = 27381.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081512 restraints weight = 13049.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.083717 restraints weight = 7808.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085560 restraints weight = 5637.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086845 restraints weight = 4190.268| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15019 Z= 0.171 Angle : 0.691 11.524 20470 Z= 0.350 Chirality : 0.039 0.201 2461 Planarity : 0.006 0.057 2668 Dihedral : 6.716 53.143 2047 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.76 % Allowed : 27.38 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.67 (0.19), residues: 1840 helix: 3.91 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -3.25 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 61 TYR 0.018 0.002 TYR W 57 PHE 0.006 0.001 PHE V 19 TRP 0.010 0.002 TRP C 10 Details of bonding type rmsd covalent geometry : bond 0.00395 (15019) covalent geometry : angle 0.69074 (20470) hydrogen bonds : bond 0.05163 ( 1288) hydrogen bonds : angle 3.63812 ( 3864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 962 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8366 (mm-30) REVERT: A 60 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8291 (t80) REVERT: A 79 ILE cc_start: 0.9104 (mm) cc_final: 0.8818 (mm) REVERT: B 27 GLN cc_start: 0.9263 (mt0) cc_final: 0.8853 (mt0) REVERT: B 35 ASP cc_start: 0.8525 (m-30) cc_final: 0.8319 (p0) REVERT: B 36 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8849 (mtpt) REVERT: C 21 ASP cc_start: 0.8570 (m-30) cc_final: 0.8167 (m-30) REVERT: C 23 THR cc_start: 0.9295 (m) cc_final: 0.8580 (p) REVERT: C 27 GLN cc_start: 0.8882 (mt0) cc_final: 0.8250 (mp10) REVERT: C 32 LEU cc_start: 0.9328 (mm) cc_final: 0.8964 (mm) REVERT: C 40 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8170 (p0) REVERT: C 56 GLU cc_start: 0.8837 (tt0) cc_final: 0.8555 (mm-30) REVERT: C 60 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.7571 (t80) REVERT: D 27 GLN cc_start: 0.9065 (mt0) cc_final: 0.8675 (mt0) REVERT: D 32 LEU cc_start: 0.9449 (mm) cc_final: 0.9106 (mm) REVERT: D 42 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8093 (m) REVERT: D 50 TYR cc_start: 0.8885 (t80) cc_final: 0.8515 (t80) REVERT: D 56 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8721 (mm-30) REVERT: D 80 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8721 (tp-100) REVERT: E 27 GLN cc_start: 0.9062 (mt0) cc_final: 0.8733 (mt0) REVERT: E 67 THR cc_start: 0.9407 (t) cc_final: 0.9144 (p) REVERT: F 24 GLN cc_start: 0.8121 (pm20) cc_final: 0.7838 (pm20) REVERT: F 45 GLN cc_start: 0.8786 (tp40) cc_final: 0.8010 (tm-30) REVERT: F 49 GLU cc_start: 0.8603 (mt-10) cc_final: 0.7547 (mt-10) REVERT: G 21 ASP cc_start: 0.8544 (m-30) cc_final: 0.7927 (m-30) REVERT: G 24 GLN cc_start: 0.8270 (pm20) cc_final: 0.7830 (pm20) REVERT: G 45 GLN cc_start: 0.8715 (tp40) cc_final: 0.8091 (tm-30) REVERT: G 49 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7519 (mt-10) REVERT: G 56 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8345 (mm-30) REVERT: G 72 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8014 (ttmt) REVERT: H 20 ASP cc_start: 0.8936 (m-30) cc_final: 0.8619 (m-30) REVERT: H 23 THR cc_start: 0.9270 (m) cc_final: 0.8860 (p) REVERT: H 56 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8622 (mm-30) REVERT: H 72 LYS cc_start: 0.8913 (ttpt) cc_final: 0.7983 (ttmt) REVERT: I 20 ASP cc_start: 0.8920 (m-30) cc_final: 0.8537 (m-30) REVERT: I 23 THR cc_start: 0.9155 (m) cc_final: 0.8896 (p) REVERT: I 27 GLN cc_start: 0.9083 (mt0) cc_final: 0.8820 (mt0) REVERT: I 56 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8462 (mm-30) REVERT: I 60 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.7962 (t80) REVERT: I 72 LYS cc_start: 0.8972 (ttpt) cc_final: 0.7952 (ttmt) REVERT: J 45 GLN cc_start: 0.8934 (tp40) cc_final: 0.8285 (tm-30) REVERT: J 56 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8607 (mm-30) REVERT: J 72 LYS cc_start: 0.8973 (ttpt) cc_final: 0.7922 (ttmt) REVERT: K 21 ASP cc_start: 0.8556 (m-30) cc_final: 0.8088 (m-30) REVERT: K 56 GLU cc_start: 0.8965 (tt0) cc_final: 0.8598 (mt-10) REVERT: K 60 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7468 (t80) REVERT: K 72 LYS cc_start: 0.8993 (ttpt) cc_final: 0.7979 (ttmt) REVERT: L 8 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8334 (t0) REVERT: L 23 THR cc_start: 0.8963 (p) cc_final: 0.8739 (p) REVERT: L 45 GLN cc_start: 0.8326 (tp40) cc_final: 0.7959 (tm-30) REVERT: L 49 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7667 (mt-10) REVERT: L 56 GLU cc_start: 0.9160 (tt0) cc_final: 0.8828 (mt-10) REVERT: L 60 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7611 (t80) REVERT: L 72 LYS cc_start: 0.8772 (ttpt) cc_final: 0.7833 (ttmt) REVERT: M 21 ASP cc_start: 0.8630 (m-30) cc_final: 0.8304 (m-30) REVERT: M 56 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8478 (mm-30) REVERT: M 80 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8854 (tp-100) REVERT: N 21 ASP cc_start: 0.8630 (m-30) cc_final: 0.8016 (m-30) REVERT: N 24 GLN cc_start: 0.8665 (pm20) cc_final: 0.8426 (pm20) REVERT: N 27 GLN cc_start: 0.8976 (mt0) cc_final: 0.8689 (mt0) REVERT: N 42 SER cc_start: 0.8809 (p) cc_final: 0.8108 (m) REVERT: N 45 GLN cc_start: 0.8841 (tp40) cc_final: 0.8574 (tm-30) REVERT: N 56 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8086 (mm-30) REVERT: O 21 ASP cc_start: 0.8400 (m-30) cc_final: 0.7682 (m-30) REVERT: O 23 THR cc_start: 0.9258 (m) cc_final: 0.8837 (p) REVERT: O 24 GLN cc_start: 0.8639 (pm20) cc_final: 0.8404 (pm20) REVERT: O 45 GLN cc_start: 0.8686 (tp40) cc_final: 0.8013 (tm-30) REVERT: O 49 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7543 (mt-10) REVERT: O 56 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8462 (mm-30) REVERT: O 80 GLN cc_start: 0.8973 (tt0) cc_final: 0.8671 (tp-100) REVERT: P 56 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8120 (mm-30) REVERT: P 67 THR cc_start: 0.9363 (m) cc_final: 0.9041 (m) REVERT: P 80 GLN cc_start: 0.9100 (tp40) cc_final: 0.8806 (tp-100) REVERT: Q 24 GLN cc_start: 0.8297 (pm20) cc_final: 0.7987 (pm20) REVERT: Q 35 ASP cc_start: 0.8799 (m-30) cc_final: 0.8566 (m-30) REVERT: Q 49 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7228 (mt-10) REVERT: R 29 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8073 (mt-10) REVERT: R 32 LEU cc_start: 0.9317 (mt) cc_final: 0.8868 (mm) REVERT: R 45 GLN cc_start: 0.8557 (tp40) cc_final: 0.7881 (tp40) REVERT: R 56 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6179 (mt-10) REVERT: R 60 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8656 (t80) REVERT: R 80 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8574 (tp-100) REVERT: S 56 GLU cc_start: 0.8842 (tt0) cc_final: 0.8126 (mm-30) REVERT: S 69 LYS cc_start: 0.8631 (tptp) cc_final: 0.7485 (mttm) REVERT: T 18 THR cc_start: 0.8774 (m) cc_final: 0.8574 (m) REVERT: T 27 GLN cc_start: 0.8551 (mt0) cc_final: 0.7953 (tm-30) REVERT: T 60 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7685 (t80) REVERT: T 69 LYS cc_start: 0.8545 (tptp) cc_final: 0.7500 (mttt) REVERT: T 79 ILE cc_start: 0.9250 (mm) cc_final: 0.8934 (mm) REVERT: U 23 THR cc_start: 0.9268 (m) cc_final: 0.8663 (p) REVERT: U 27 GLN cc_start: 0.8701 (mt0) cc_final: 0.8221 (tm-30) REVERT: U 55 SER cc_start: 0.8932 (m) cc_final: 0.8707 (m) REVERT: U 56 GLU cc_start: 0.8710 (tt0) cc_final: 0.8316 (mm-30) REVERT: U 69 LYS cc_start: 0.8658 (tptp) cc_final: 0.7377 (mttm) REVERT: V 21 ASP cc_start: 0.8724 (m-30) cc_final: 0.8354 (m-30) REVERT: V 39 LYS cc_start: 0.9206 (mmmt) cc_final: 0.9006 (mmmm) REVERT: V 60 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.8375 (t80) REVERT: W 16 SER cc_start: 0.8783 (m) cc_final: 0.8467 (m) REVERT: W 21 ASP cc_start: 0.8563 (m-30) cc_final: 0.7984 (m-30) REVERT: W 23 THR cc_start: 0.9361 (m) cc_final: 0.9083 (p) REVERT: W 24 GLN cc_start: 0.8420 (pm20) cc_final: 0.8018 (pm20) REVERT: W 69 LYS cc_start: 0.8598 (tptp) cc_final: 0.8005 (ttmt) REVERT: W 80 GLN cc_start: 0.8905 (tt0) cc_final: 0.8612 (tp-100) outliers start: 115 outliers final: 82 residues processed: 1016 average time/residue: 0.0977 time to fit residues: 154.7224 Evaluate side-chains 1048 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 955 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 60 TYR Chi-restraints excluded: chain W residue 68 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 87 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 100 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN P 40 ASN R 40 ASN S 80 GLN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080913 restraints weight = 26868.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084428 restraints weight = 12773.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086949 restraints weight = 7618.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088699 restraints weight = 5167.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090004 restraints weight = 3858.402| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15019 Z= 0.145 Angle : 0.700 12.112 20470 Z= 0.347 Chirality : 0.038 0.205 2461 Planarity : 0.006 0.053 2668 Dihedral : 6.677 52.658 2047 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.82 % Allowed : 29.32 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.69 (0.19), residues: 1840 helix: 3.90 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -3.09 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 61 TYR 0.022 0.001 TYR J 50 PHE 0.004 0.001 PHE R 82 TRP 0.010 0.002 TRP C 10 Details of bonding type rmsd covalent geometry : bond 0.00321 (15019) covalent geometry : angle 0.70036 (20470) hydrogen bonds : bond 0.04817 ( 1288) hydrogen bonds : angle 3.49511 ( 3864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 970 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9118 (mt0) cc_final: 0.8598 (mt0) REVERT: A 56 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8348 (mm-30) REVERT: A 60 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8427 (t80) REVERT: B 27 GLN cc_start: 0.9180 (mt0) cc_final: 0.8830 (mt0) REVERT: C 21 ASP cc_start: 0.8480 (m-30) cc_final: 0.8068 (m-30) REVERT: C 23 THR cc_start: 0.9220 (m) cc_final: 0.8499 (p) REVERT: C 27 GLN cc_start: 0.8862 (mt0) cc_final: 0.8276 (mp10) REVERT: C 56 GLU cc_start: 0.8784 (tt0) cc_final: 0.8559 (mm-30) REVERT: C 60 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7566 (t80) REVERT: D 27 GLN cc_start: 0.8965 (mt0) cc_final: 0.8615 (mt0) REVERT: D 42 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8007 (m) REVERT: D 56 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8642 (mm-30) REVERT: E 27 GLN cc_start: 0.8872 (mt0) cc_final: 0.8631 (mt0) REVERT: E 42 SER cc_start: 0.9361 (m) cc_final: 0.8431 (m) REVERT: E 67 THR cc_start: 0.9415 (t) cc_final: 0.9115 (p) REVERT: F 21 ASP cc_start: 0.8116 (m-30) cc_final: 0.7899 (m-30) REVERT: F 24 GLN cc_start: 0.8062 (pm20) cc_final: 0.7763 (pm20) REVERT: F 45 GLN cc_start: 0.8694 (tp40) cc_final: 0.7903 (tm-30) REVERT: G 21 ASP cc_start: 0.8509 (m-30) cc_final: 0.7893 (m-30) REVERT: G 24 GLN cc_start: 0.8379 (pm20) cc_final: 0.8012 (pm20) REVERT: G 45 GLN cc_start: 0.8553 (tp40) cc_final: 0.7993 (tm-30) REVERT: G 49 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7533 (mt-10) REVERT: G 56 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8352 (mm-30) REVERT: G 59 LEU cc_start: 0.9401 (mm) cc_final: 0.9198 (mt) REVERT: G 72 LYS cc_start: 0.8868 (ttpt) cc_final: 0.7488 (tttt) REVERT: H 20 ASP cc_start: 0.8966 (m-30) cc_final: 0.8616 (m-30) REVERT: H 23 THR cc_start: 0.9189 (m) cc_final: 0.8832 (p) REVERT: H 56 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8499 (mm-30) REVERT: H 72 LYS cc_start: 0.8913 (ttpt) cc_final: 0.7853 (ttmt) REVERT: H 80 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8698 (tp-100) REVERT: I 20 ASP cc_start: 0.8905 (m-30) cc_final: 0.8543 (m-30) REVERT: I 23 THR cc_start: 0.9134 (m) cc_final: 0.8901 (p) REVERT: I 56 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8478 (mm-30) REVERT: I 60 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8042 (t80) REVERT: I 72 LYS cc_start: 0.8959 (ttpt) cc_final: 0.8055 (ttmt) REVERT: J 39 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8965 (mmmt) REVERT: J 45 GLN cc_start: 0.8812 (tp40) cc_final: 0.8160 (tm-30) REVERT: J 56 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8553 (mm-30) REVERT: J 72 LYS cc_start: 0.8859 (ttpt) cc_final: 0.7865 (ttmt) REVERT: J 80 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8759 (tp40) REVERT: K 21 ASP cc_start: 0.8443 (m-30) cc_final: 0.8017 (m-30) REVERT: K 56 GLU cc_start: 0.8919 (tt0) cc_final: 0.8599 (mt-10) REVERT: K 60 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7641 (t80) REVERT: K 72 LYS cc_start: 0.8984 (ttpt) cc_final: 0.7936 (ttmt) REVERT: L 8 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8405 (t0) REVERT: L 32 LEU cc_start: 0.9335 (mm) cc_final: 0.8947 (mm) REVERT: L 40 ASN cc_start: 0.8571 (p0) cc_final: 0.8251 (p0) REVERT: L 49 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7941 (mt-10) REVERT: L 56 GLU cc_start: 0.9154 (tt0) cc_final: 0.8834 (mt-10) REVERT: L 60 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.7710 (t80) REVERT: L 72 LYS cc_start: 0.8767 (ttpt) cc_final: 0.7755 (ttmt) REVERT: M 21 ASP cc_start: 0.8580 (m-30) cc_final: 0.8270 (m-30) REVERT: M 27 GLN cc_start: 0.9078 (mt0) cc_final: 0.8524 (mp10) REVERT: M 56 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8443 (mm-30) REVERT: N 10 TRP cc_start: 0.8709 (p-90) cc_final: 0.7945 (p-90) REVERT: N 20 ASP cc_start: 0.8986 (m-30) cc_final: 0.8773 (m-30) REVERT: N 21 ASP cc_start: 0.8580 (m-30) cc_final: 0.8055 (m-30) REVERT: N 27 GLN cc_start: 0.8972 (mt0) cc_final: 0.8678 (mt0) REVERT: N 45 GLN cc_start: 0.8704 (tp40) cc_final: 0.8272 (tm-30) REVERT: N 56 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8038 (mm-30) REVERT: O 21 ASP cc_start: 0.8482 (m-30) cc_final: 0.7719 (m-30) REVERT: O 23 THR cc_start: 0.9198 (m) cc_final: 0.8814 (p) REVERT: O 24 GLN cc_start: 0.8639 (pm20) cc_final: 0.8387 (pm20) REVERT: O 45 GLN cc_start: 0.8681 (tp40) cc_final: 0.7846 (tm-30) REVERT: O 49 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7364 (mt-10) REVERT: O 56 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8443 (mm-30) REVERT: P 35 ASP cc_start: 0.8932 (m-30) cc_final: 0.8667 (m-30) REVERT: P 56 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8125 (mm-30) REVERT: P 67 THR cc_start: 0.9332 (m) cc_final: 0.8926 (m) REVERT: P 80 GLN cc_start: 0.9009 (tp40) cc_final: 0.8624 (tp-100) REVERT: Q 24 GLN cc_start: 0.8422 (pm20) cc_final: 0.8101 (pm20) REVERT: Q 35 ASP cc_start: 0.8857 (m-30) cc_final: 0.8496 (m-30) REVERT: Q 49 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7921 (mt-10) REVERT: R 29 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7983 (mt-10) REVERT: R 56 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6866 (mm-30) REVERT: R 60 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8617 (t80) REVERT: R 66 ASN cc_start: 0.8853 (m-40) cc_final: 0.8549 (m-40) REVERT: R 80 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8574 (tp-100) REVERT: S 56 GLU cc_start: 0.8798 (tt0) cc_final: 0.8057 (mm-30) REVERT: S 69 LYS cc_start: 0.8635 (tptp) cc_final: 0.7494 (mttm) REVERT: T 27 GLN cc_start: 0.8545 (mt0) cc_final: 0.7950 (tm-30) REVERT: T 45 GLN cc_start: 0.8347 (tp40) cc_final: 0.8045 (tm-30) REVERT: T 60 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7671 (t80) REVERT: T 69 LYS cc_start: 0.8482 (tptp) cc_final: 0.7386 (mttt) REVERT: U 23 THR cc_start: 0.9283 (m) cc_final: 0.8691 (p) REVERT: U 27 GLN cc_start: 0.8704 (mt0) cc_final: 0.8203 (tm-30) REVERT: U 55 SER cc_start: 0.8917 (m) cc_final: 0.8697 (m) REVERT: U 56 GLU cc_start: 0.8661 (tt0) cc_final: 0.8025 (mm-30) REVERT: U 61 ARG cc_start: 0.8853 (mmt180) cc_final: 0.8599 (mmt-90) REVERT: U 69 LYS cc_start: 0.8698 (tptp) cc_final: 0.7818 (ttmt) REVERT: V 14 SER cc_start: 0.9125 (t) cc_final: 0.8610 (p) REVERT: V 21 ASP cc_start: 0.8631 (m-30) cc_final: 0.8323 (m-30) REVERT: V 60 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8392 (t80) REVERT: V 69 LYS cc_start: 0.8577 (tptp) cc_final: 0.7359 (mttm) REVERT: W 16 SER cc_start: 0.8606 (m) cc_final: 0.8361 (m) REVERT: W 21 ASP cc_start: 0.8507 (m-30) cc_final: 0.7987 (m-30) REVERT: W 23 THR cc_start: 0.9339 (m) cc_final: 0.9111 (p) REVERT: W 69 LYS cc_start: 0.8617 (tptp) cc_final: 0.8020 (ttmt) outliers start: 99 outliers final: 60 residues processed: 1018 average time/residue: 0.0992 time to fit residues: 157.1194 Evaluate side-chains 1024 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 954 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 143 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 ASN E 40 ASN F 40 ASN L 80 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN Q 40 ASN R 40 ASN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.092880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.076021 restraints weight = 27791.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079325 restraints weight = 13480.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081651 restraints weight = 8168.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.083363 restraints weight = 5676.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.084552 restraints weight = 4292.898| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15019 Z= 0.215 Angle : 0.747 13.292 20470 Z= 0.387 Chirality : 0.041 0.201 2461 Planarity : 0.007 0.060 2668 Dihedral : 6.847 53.567 2047 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 7.17 % Allowed : 29.73 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.49 (0.19), residues: 1840 helix: 3.74 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.95 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 61 TYR 0.027 0.002 TYR T 50 PHE 0.005 0.001 PHE G 19 TRP 0.006 0.002 TRP N 10 Details of bonding type rmsd covalent geometry : bond 0.00510 (15019) covalent geometry : angle 0.74748 (20470) hydrogen bonds : bond 0.05497 ( 1288) hydrogen bonds : angle 3.84243 ( 3864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 963 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9091 (mt0) cc_final: 0.8693 (mt0) REVERT: A 56 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8256 (mm-30) REVERT: A 60 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8422 (t80) REVERT: B 27 GLN cc_start: 0.9185 (mt0) cc_final: 0.8832 (mt0) REVERT: B 45 GLN cc_start: 0.8975 (tp40) cc_final: 0.8764 (tp40) REVERT: C 21 ASP cc_start: 0.8531 (m-30) cc_final: 0.8109 (m-30) REVERT: C 23 THR cc_start: 0.9193 (m) cc_final: 0.8461 (p) REVERT: C 27 GLN cc_start: 0.8922 (mt0) cc_final: 0.8315 (mp10) REVERT: C 56 GLU cc_start: 0.8880 (tt0) cc_final: 0.8557 (mm-30) REVERT: C 60 TYR cc_start: 0.9016 (OUTLIER) cc_final: 0.7517 (t80) REVERT: D 27 GLN cc_start: 0.8996 (mt0) cc_final: 0.8652 (mt0) REVERT: D 42 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8009 (m) REVERT: D 50 TYR cc_start: 0.8939 (t80) cc_final: 0.8440 (t80) REVERT: E 27 GLN cc_start: 0.8964 (mt0) cc_final: 0.8447 (mt0) REVERT: E 55 SER cc_start: 0.9035 (m) cc_final: 0.8639 (p) REVERT: E 67 THR cc_start: 0.9405 (t) cc_final: 0.9131 (p) REVERT: F 24 GLN cc_start: 0.8283 (pm20) cc_final: 0.7912 (pm20) REVERT: F 45 GLN cc_start: 0.8811 (tp40) cc_final: 0.7986 (tm-30) REVERT: F 49 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7595 (mt-10) REVERT: G 21 ASP cc_start: 0.8577 (m-30) cc_final: 0.8096 (m-30) REVERT: G 45 GLN cc_start: 0.8778 (tp40) cc_final: 0.8115 (tm-30) REVERT: G 49 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7603 (mt-10) REVERT: G 56 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8263 (mm-30) REVERT: G 59 LEU cc_start: 0.9461 (mm) cc_final: 0.9213 (mt) REVERT: G 72 LYS cc_start: 0.9039 (ttpt) cc_final: 0.7988 (ttmt) REVERT: H 20 ASP cc_start: 0.9010 (m-30) cc_final: 0.8666 (m-30) REVERT: H 23 THR cc_start: 0.9216 (m) cc_final: 0.8850 (p) REVERT: H 56 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8615 (mm-30) REVERT: H 72 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8124 (ttmt) REVERT: H 80 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8692 (tp-100) REVERT: I 20 ASP cc_start: 0.8928 (m-30) cc_final: 0.8662 (m-30) REVERT: I 23 THR cc_start: 0.9192 (m) cc_final: 0.8964 (p) REVERT: I 45 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8177 (tm-30) REVERT: I 60 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8244 (t80) REVERT: I 72 LYS cc_start: 0.9033 (ttpt) cc_final: 0.7936 (ttmt) REVERT: J 27 GLN cc_start: 0.9186 (mt0) cc_final: 0.8978 (mt0) REVERT: J 39 LYS cc_start: 0.9362 (mmtt) cc_final: 0.8974 (mmmt) REVERT: J 45 GLN cc_start: 0.8914 (tp40) cc_final: 0.8481 (tm-30) REVERT: J 56 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8532 (mm-30) REVERT: J 72 LYS cc_start: 0.8889 (ttpt) cc_final: 0.7835 (ttmt) REVERT: K 21 ASP cc_start: 0.8492 (m-30) cc_final: 0.8095 (m-30) REVERT: K 56 GLU cc_start: 0.8949 (tt0) cc_final: 0.8583 (mt-10) REVERT: K 60 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.7513 (t80) REVERT: K 72 LYS cc_start: 0.9027 (ttpt) cc_final: 0.7976 (ttmt) REVERT: L 32 LEU cc_start: 0.9424 (mm) cc_final: 0.9212 (mm) REVERT: L 40 ASN cc_start: 0.8622 (p0) cc_final: 0.8369 (p0) REVERT: L 45 GLN cc_start: 0.8675 (tp40) cc_final: 0.7872 (tm-30) REVERT: L 49 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8061 (mt-10) REVERT: L 56 GLU cc_start: 0.9245 (tt0) cc_final: 0.8835 (mt-10) REVERT: L 60 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.7645 (t80) REVERT: L 72 LYS cc_start: 0.8804 (ttpt) cc_final: 0.7843 (ttmt) REVERT: M 21 ASP cc_start: 0.8695 (m-30) cc_final: 0.8451 (m-30) REVERT: M 27 GLN cc_start: 0.9133 (mt0) cc_final: 0.8512 (mp10) REVERT: M 56 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8457 (mm-30) REVERT: N 10 TRP cc_start: 0.8896 (p-90) cc_final: 0.8231 (p-90) REVERT: N 20 ASP cc_start: 0.9083 (m-30) cc_final: 0.8773 (m-30) REVERT: N 21 ASP cc_start: 0.8599 (m-30) cc_final: 0.8352 (m-30) REVERT: N 27 GLN cc_start: 0.9019 (mt0) cc_final: 0.8683 (mt0) REVERT: N 45 GLN cc_start: 0.8827 (tp40) cc_final: 0.8406 (tm-30) REVERT: N 56 GLU cc_start: 0.8817 (mt-10) cc_final: 0.7879 (mm-30) REVERT: O 21 ASP cc_start: 0.8510 (m-30) cc_final: 0.7825 (m-30) REVERT: O 24 GLN cc_start: 0.8737 (pm20) cc_final: 0.8440 (pm20) REVERT: O 45 GLN cc_start: 0.8737 (tp40) cc_final: 0.8010 (tm-30) REVERT: O 49 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7586 (mt-10) REVERT: O 56 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8473 (mm-30) REVERT: P 35 ASP cc_start: 0.8916 (m-30) cc_final: 0.8632 (m-30) REVERT: P 45 GLN cc_start: 0.8621 (tp40) cc_final: 0.8117 (tm-30) REVERT: P 56 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8100 (mm-30) REVERT: P 67 THR cc_start: 0.9282 (m) cc_final: 0.8995 (m) REVERT: P 80 GLN cc_start: 0.9018 (tp40) cc_final: 0.8598 (tp-100) REVERT: Q 24 GLN cc_start: 0.8421 (pm20) cc_final: 0.8110 (pm20) REVERT: Q 35 ASP cc_start: 0.8873 (m-30) cc_final: 0.8440 (m-30) REVERT: Q 49 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7978 (mt-10) REVERT: Q 50 TYR cc_start: 0.8950 (t80) cc_final: 0.8473 (t80) REVERT: R 29 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8006 (mt-10) REVERT: R 45 GLN cc_start: 0.8529 (tp40) cc_final: 0.7854 (tp40) REVERT: R 56 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6165 (mt-10) REVERT: R 60 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8589 (t80) REVERT: R 80 GLN cc_start: 0.9027 (tp-100) cc_final: 0.8603 (tp-100) REVERT: S 27 GLN cc_start: 0.9043 (mt0) cc_final: 0.8331 (tm-30) REVERT: S 56 GLU cc_start: 0.8880 (tt0) cc_final: 0.8262 (mm-30) REVERT: S 69 LYS cc_start: 0.8656 (tptp) cc_final: 0.7579 (mttm) REVERT: T 27 GLN cc_start: 0.8607 (mt0) cc_final: 0.8015 (tm-30) REVERT: T 60 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.7827 (t80) REVERT: T 69 LYS cc_start: 0.8470 (tptp) cc_final: 0.7378 (mttt) REVERT: U 23 THR cc_start: 0.9298 (m) cc_final: 0.8678 (p) REVERT: U 27 GLN cc_start: 0.8723 (mt0) cc_final: 0.8243 (tm-30) REVERT: U 61 ARG cc_start: 0.8904 (mmt180) cc_final: 0.8670 (mmt-90) REVERT: U 69 LYS cc_start: 0.8557 (tptp) cc_final: 0.7254 (mttm) REVERT: V 21 ASP cc_start: 0.8705 (m-30) cc_final: 0.8380 (m-30) REVERT: V 60 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8409 (t80) REVERT: W 21 ASP cc_start: 0.8665 (m-30) cc_final: 0.8315 (m-30) REVERT: W 23 THR cc_start: 0.9299 (m) cc_final: 0.9013 (p) REVERT: W 24 GLN cc_start: 0.8439 (pm20) cc_final: 0.8152 (pm20) REVERT: W 45 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8266 (tm-30) REVERT: W 69 LYS cc_start: 0.8692 (tptp) cc_final: 0.8033 (ttmt) outliers start: 122 outliers final: 92 residues processed: 1019 average time/residue: 0.1007 time to fit residues: 158.2168 Evaluate side-chains 1057 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 956 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 15 LEU Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 60 TYR Chi-restraints excluded: chain W residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN P 40 ASN Q 40 ASN R 40 ASN S 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079445 restraints weight = 26840.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082893 restraints weight = 12960.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085441 restraints weight = 7807.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087220 restraints weight = 5386.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088520 restraints weight = 4042.575| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15019 Z= 0.161 Angle : 0.762 14.000 20470 Z= 0.382 Chirality : 0.040 0.242 2461 Planarity : 0.006 0.057 2668 Dihedral : 6.792 53.180 2047 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.17 % Allowed : 32.49 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.43 (0.19), residues: 1840 helix: 3.68 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.84 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 61 TYR 0.023 0.001 TYR T 50 PHE 0.005 0.001 PHE M 19 TRP 0.010 0.002 TRP C 10 Details of bonding type rmsd covalent geometry : bond 0.00365 (15019) covalent geometry : angle 0.76155 (20470) hydrogen bonds : bond 0.05074 ( 1288) hydrogen bonds : angle 3.66342 ( 3864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 957 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9101 (mt0) cc_final: 0.8765 (mt0) REVERT: A 56 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8235 (mm-30) REVERT: A 60 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8436 (t80) REVERT: B 27 GLN cc_start: 0.9191 (mt0) cc_final: 0.8947 (mt0) REVERT: B 45 GLN cc_start: 0.8826 (tp40) cc_final: 0.8557 (tp40) REVERT: C 21 ASP cc_start: 0.8465 (m-30) cc_final: 0.8054 (m-30) REVERT: C 23 THR cc_start: 0.9163 (m) cc_final: 0.8366 (p) REVERT: C 27 GLN cc_start: 0.8900 (mt0) cc_final: 0.8426 (mp10) REVERT: C 50 TYR cc_start: 0.9105 (t80) cc_final: 0.8805 (t80) REVERT: C 56 GLU cc_start: 0.8802 (tt0) cc_final: 0.8521 (mm-30) REVERT: C 60 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7573 (t80) REVERT: D 20 ASP cc_start: 0.9054 (m-30) cc_final: 0.8830 (m-30) REVERT: D 27 GLN cc_start: 0.8881 (mt0) cc_final: 0.8409 (mt0) REVERT: D 42 SER cc_start: 0.8875 (OUTLIER) cc_final: 0.8106 (m) REVERT: D 56 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8676 (mm-30) REVERT: E 27 GLN cc_start: 0.8930 (mt0) cc_final: 0.8404 (mt0) REVERT: E 42 SER cc_start: 0.9265 (m) cc_final: 0.8280 (m) REVERT: E 67 THR cc_start: 0.9410 (t) cc_final: 0.9144 (p) REVERT: F 24 GLN cc_start: 0.8290 (pm20) cc_final: 0.7899 (pm20) REVERT: F 45 GLN cc_start: 0.8741 (tp40) cc_final: 0.7919 (tm-30) REVERT: G 21 ASP cc_start: 0.8553 (m-30) cc_final: 0.8234 (m-30) REVERT: G 45 GLN cc_start: 0.8612 (tp40) cc_final: 0.8027 (tm-30) REVERT: G 49 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7556 (mt-10) REVERT: G 56 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8297 (mm-30) REVERT: G 59 LEU cc_start: 0.9425 (mm) cc_final: 0.9190 (mt) REVERT: G 72 LYS cc_start: 0.8992 (ttpt) cc_final: 0.7894 (ttmt) REVERT: H 20 ASP cc_start: 0.9013 (m-30) cc_final: 0.8649 (m-30) REVERT: H 23 THR cc_start: 0.9105 (m) cc_final: 0.8751 (p) REVERT: H 56 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8574 (mm-30) REVERT: H 72 LYS cc_start: 0.8901 (ttpt) cc_final: 0.7888 (ttmt) REVERT: H 80 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8734 (tp-100) REVERT: I 20 ASP cc_start: 0.8907 (m-30) cc_final: 0.8633 (m-30) REVERT: I 23 THR cc_start: 0.9140 (m) cc_final: 0.8890 (p) REVERT: I 45 GLN cc_start: 0.8671 (tm-30) cc_final: 0.7995 (tm-30) REVERT: I 56 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8517 (mm-30) REVERT: I 60 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.7917 (t80) REVERT: I 72 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8046 (ttmt) REVERT: J 39 LYS cc_start: 0.9323 (mmtt) cc_final: 0.8954 (mmmt) REVERT: J 56 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8513 (mm-30) REVERT: J 72 LYS cc_start: 0.8890 (ttpt) cc_final: 0.7840 (ttmt) REVERT: K 21 ASP cc_start: 0.8515 (m-30) cc_final: 0.8194 (m-30) REVERT: K 56 GLU cc_start: 0.8920 (tt0) cc_final: 0.8563 (mt-10) REVERT: K 72 LYS cc_start: 0.9007 (ttpt) cc_final: 0.8021 (ttmt) REVERT: L 40 ASN cc_start: 0.8542 (p0) cc_final: 0.8261 (p0) REVERT: L 45 GLN cc_start: 0.8540 (tp40) cc_final: 0.7998 (tp40) REVERT: L 54 LEU cc_start: 0.8749 (tt) cc_final: 0.8535 (tt) REVERT: L 56 GLU cc_start: 0.9183 (tt0) cc_final: 0.8785 (mt-10) REVERT: L 60 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.7680 (t80) REVERT: L 72 LYS cc_start: 0.8756 (ttpt) cc_final: 0.7697 (ttmt) REVERT: M 21 ASP cc_start: 0.8641 (m-30) cc_final: 0.8401 (m-30) REVERT: M 27 GLN cc_start: 0.9072 (mt0) cc_final: 0.8464 (mp10) REVERT: M 56 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8402 (mm-30) REVERT: M 79 ILE cc_start: 0.8905 (mm) cc_final: 0.8606 (mm) REVERT: N 10 TRP cc_start: 0.8771 (p-90) cc_final: 0.8024 (p-90) REVERT: N 20 ASP cc_start: 0.9128 (m-30) cc_final: 0.8694 (m-30) REVERT: N 27 GLN cc_start: 0.9052 (mt0) cc_final: 0.8478 (mt0) REVERT: N 56 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8049 (mm-30) REVERT: O 21 ASP cc_start: 0.8466 (m-30) cc_final: 0.7736 (m-30) REVERT: O 24 GLN cc_start: 0.8766 (pm20) cc_final: 0.8462 (pm20) REVERT: O 45 GLN cc_start: 0.8510 (tp40) cc_final: 0.7829 (tm-30) REVERT: O 49 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7463 (mt-10) REVERT: O 56 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8414 (mm-30) REVERT: P 35 ASP cc_start: 0.8887 (m-30) cc_final: 0.8566 (m-30) REVERT: P 45 GLN cc_start: 0.8511 (tp40) cc_final: 0.8044 (tm-30) REVERT: P 56 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8101 (mm-30) REVERT: P 67 THR cc_start: 0.9270 (m) cc_final: 0.8983 (m) REVERT: P 80 GLN cc_start: 0.8997 (tp40) cc_final: 0.8626 (tp-100) REVERT: Q 24 GLN cc_start: 0.8532 (pm20) cc_final: 0.8176 (pm20) REVERT: Q 35 ASP cc_start: 0.8855 (m-30) cc_final: 0.8437 (m-30) REVERT: R 60 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8577 (t80) REVERT: R 66 ASN cc_start: 0.8896 (m-40) cc_final: 0.8603 (m-40) REVERT: R 80 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8616 (tp40) REVERT: S 27 GLN cc_start: 0.8701 (mt0) cc_final: 0.8147 (tm-30) REVERT: S 56 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8114 (mm-30) REVERT: S 69 LYS cc_start: 0.8633 (tptp) cc_final: 0.7496 (mttm) REVERT: T 27 GLN cc_start: 0.8603 (mt0) cc_final: 0.8085 (tm-30) REVERT: T 45 GLN cc_start: 0.8375 (tp40) cc_final: 0.8087 (tm-30) REVERT: T 69 LYS cc_start: 0.8456 (tptp) cc_final: 0.7342 (mttt) REVERT: U 23 THR cc_start: 0.9245 (m) cc_final: 0.8623 (p) REVERT: U 27 GLN cc_start: 0.8718 (mt0) cc_final: 0.8227 (tm-30) REVERT: U 56 GLU cc_start: 0.8718 (tt0) cc_final: 0.8029 (mm-30) REVERT: U 61 ARG cc_start: 0.8862 (mmt180) cc_final: 0.8643 (mmt-90) REVERT: U 69 LYS cc_start: 0.8566 (tptp) cc_final: 0.7271 (mttm) REVERT: V 21 ASP cc_start: 0.8648 (m-30) cc_final: 0.8356 (m-30) REVERT: V 60 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8288 (t80) REVERT: W 10 TRP cc_start: 0.8773 (p-90) cc_final: 0.8130 (p-90) REVERT: W 23 THR cc_start: 0.9322 (m) cc_final: 0.9048 (p) REVERT: W 45 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8154 (tm-30) REVERT: W 69 LYS cc_start: 0.8699 (tptp) cc_final: 0.8020 (ttmt) outliers start: 88 outliers final: 62 residues processed: 999 average time/residue: 0.0973 time to fit residues: 150.8281 Evaluate side-chains 1022 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 952 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN P 40 ASN Q 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.079023 restraints weight = 27097.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.082488 restraints weight = 13053.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084661 restraints weight = 7843.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086575 restraints weight = 5627.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087733 restraints weight = 4183.672| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15019 Z= 0.175 Angle : 0.781 13.815 20470 Z= 0.394 Chirality : 0.041 0.267 2461 Planarity : 0.006 0.058 2668 Dihedral : 6.740 53.260 2045 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.82 % Allowed : 32.61 % Favored : 61.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.35 (0.19), residues: 1840 helix: 3.61 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.76 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 61 TYR 0.025 0.002 TYR T 50 PHE 0.005 0.001 PHE M 19 TRP 0.011 0.002 TRP M 10 Details of bonding type rmsd covalent geometry : bond 0.00406 (15019) covalent geometry : angle 0.78116 (20470) hydrogen bonds : bond 0.05125 ( 1288) hydrogen bonds : angle 3.73028 ( 3864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 958 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9102 (mt0) cc_final: 0.8764 (mt0) REVERT: A 56 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8190 (mm-30) REVERT: A 60 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 27 GLN cc_start: 0.9137 (mt0) cc_final: 0.8838 (mt0) REVERT: B 50 TYR cc_start: 0.9005 (t80) cc_final: 0.8670 (t80) REVERT: C 21 ASP cc_start: 0.8457 (m-30) cc_final: 0.8037 (m-30) REVERT: C 23 THR cc_start: 0.9165 (m) cc_final: 0.8351 (p) REVERT: C 27 GLN cc_start: 0.8972 (mt0) cc_final: 0.8570 (mp10) REVERT: C 56 GLU cc_start: 0.8840 (tt0) cc_final: 0.8524 (mm-30) REVERT: C 60 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7497 (t80) REVERT: D 42 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8074 (m) REVERT: E 42 SER cc_start: 0.9267 (m) cc_final: 0.8165 (m) REVERT: E 67 THR cc_start: 0.9413 (t) cc_final: 0.9126 (p) REVERT: F 45 GLN cc_start: 0.8763 (tp40) cc_final: 0.7975 (tm-30) REVERT: F 49 GLU cc_start: 0.8636 (mt-10) cc_final: 0.7636 (mt-10) REVERT: G 45 GLN cc_start: 0.8645 (tp40) cc_final: 0.8018 (tm-30) REVERT: G 49 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7544 (mt-10) REVERT: G 56 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8269 (mm-30) REVERT: G 59 LEU cc_start: 0.9401 (mm) cc_final: 0.9158 (mt) REVERT: G 72 LYS cc_start: 0.9013 (ttpt) cc_final: 0.7899 (ttmt) REVERT: H 20 ASP cc_start: 0.9037 (m-30) cc_final: 0.8652 (m-30) REVERT: H 23 THR cc_start: 0.9121 (m) cc_final: 0.8734 (p) REVERT: H 56 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8591 (mm-30) REVERT: H 72 LYS cc_start: 0.8920 (ttpt) cc_final: 0.7886 (ttmt) REVERT: I 20 ASP cc_start: 0.8919 (m-30) cc_final: 0.8665 (m-30) REVERT: I 23 THR cc_start: 0.9134 (m) cc_final: 0.8878 (p) REVERT: I 45 GLN cc_start: 0.8662 (tm-30) cc_final: 0.7993 (tm-30) REVERT: I 56 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8534 (mm-30) REVERT: I 60 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.7959 (t80) REVERT: I 72 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8060 (ttmt) REVERT: J 39 LYS cc_start: 0.9335 (mmtt) cc_final: 0.8965 (mmmt) REVERT: J 56 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8443 (mt-10) REVERT: J 72 LYS cc_start: 0.8904 (ttpt) cc_final: 0.7846 (ttmt) REVERT: K 21 ASP cc_start: 0.8502 (m-30) cc_final: 0.8187 (m-30) REVERT: K 56 GLU cc_start: 0.8933 (tt0) cc_final: 0.8565 (mt-10) REVERT: K 72 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8027 (ttmt) REVERT: L 40 ASN cc_start: 0.8634 (p0) cc_final: 0.8376 (p0) REVERT: L 45 GLN cc_start: 0.8464 (tp40) cc_final: 0.8116 (tp40) REVERT: L 56 GLU cc_start: 0.9180 (tt0) cc_final: 0.8786 (mt-10) REVERT: L 60 TYR cc_start: 0.8968 (OUTLIER) cc_final: 0.7735 (t80) REVERT: L 72 LYS cc_start: 0.8769 (ttpt) cc_final: 0.7779 (ttmt) REVERT: M 21 ASP cc_start: 0.8645 (m-30) cc_final: 0.8402 (m-30) REVERT: M 27 GLN cc_start: 0.9074 (mt0) cc_final: 0.8461 (mp10) REVERT: M 56 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8421 (mm-30) REVERT: N 10 TRP cc_start: 0.8741 (p-90) cc_final: 0.7945 (p-90) REVERT: N 20 ASP cc_start: 0.9106 (m-30) cc_final: 0.8772 (m-30) REVERT: N 45 GLN cc_start: 0.8623 (tp40) cc_final: 0.8244 (tm-30) REVERT: N 56 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8108 (mm-30) REVERT: O 21 ASP cc_start: 0.8460 (m-30) cc_final: 0.7806 (m-30) REVERT: O 24 GLN cc_start: 0.8801 (pm20) cc_final: 0.8452 (pm20) REVERT: O 45 GLN cc_start: 0.8570 (tp40) cc_final: 0.7876 (tm-30) REVERT: O 49 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7436 (mt-10) REVERT: O 56 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8407 (mm-30) REVERT: P 35 ASP cc_start: 0.8885 (m-30) cc_final: 0.8550 (m-30) REVERT: P 45 GLN cc_start: 0.8530 (tp40) cc_final: 0.8062 (tm-30) REVERT: P 56 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8093 (mm-30) REVERT: P 67 THR cc_start: 0.9294 (m) cc_final: 0.8968 (m) REVERT: P 80 GLN cc_start: 0.9007 (tp40) cc_final: 0.8686 (tp-100) REVERT: Q 24 GLN cc_start: 0.8488 (pm20) cc_final: 0.8103 (pm20) REVERT: Q 35 ASP cc_start: 0.8883 (m-30) cc_final: 0.8457 (m-30) REVERT: Q 45 GLN cc_start: 0.8281 (tp40) cc_final: 0.7715 (tm-30) REVERT: R 60 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8450 (t80) REVERT: R 66 ASN cc_start: 0.8892 (m-40) cc_final: 0.8598 (m-40) REVERT: R 80 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8453 (tp-100) REVERT: S 27 GLN cc_start: 0.8722 (mt0) cc_final: 0.8172 (tm-30) REVERT: S 56 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: S 69 LYS cc_start: 0.8653 (tptp) cc_final: 0.7522 (mttm) REVERT: T 27 GLN cc_start: 0.8624 (mt0) cc_final: 0.8102 (tm-30) REVERT: T 45 GLN cc_start: 0.8396 (tp40) cc_final: 0.8089 (tm-30) REVERT: T 69 LYS cc_start: 0.8475 (tptp) cc_final: 0.7369 (mttt) REVERT: U 23 THR cc_start: 0.9249 (m) cc_final: 0.8639 (p) REVERT: U 27 GLN cc_start: 0.8728 (mt0) cc_final: 0.8237 (tm-30) REVERT: U 45 GLN cc_start: 0.8873 (tp40) cc_final: 0.8358 (tm-30) REVERT: U 61 ARG cc_start: 0.8912 (mmt180) cc_final: 0.8681 (mmt-90) REVERT: U 69 LYS cc_start: 0.8555 (tptp) cc_final: 0.7242 (mttm) REVERT: V 21 ASP cc_start: 0.8620 (m-30) cc_final: 0.8332 (m-30) REVERT: V 60 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8306 (t80) REVERT: W 10 TRP cc_start: 0.8842 (p-90) cc_final: 0.8140 (p-90) REVERT: W 21 ASP cc_start: 0.8738 (m-30) cc_final: 0.8523 (m-30) REVERT: W 23 THR cc_start: 0.9274 (m) cc_final: 0.8992 (p) REVERT: W 45 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8142 (tm-30) REVERT: W 69 LYS cc_start: 0.8723 (tptp) cc_final: 0.8037 (ttmt) outliers start: 99 outliers final: 71 residues processed: 1008 average time/residue: 0.0977 time to fit residues: 153.0531 Evaluate side-chains 1031 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 952 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 83 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN O 27 GLN P 40 ASN Q 40 ASN S 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.079653 restraints weight = 27038.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.083168 restraints weight = 12959.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085458 restraints weight = 7755.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087270 restraints weight = 5466.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088618 restraints weight = 4080.503| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15019 Z= 0.171 Angle : 0.798 13.877 20470 Z= 0.401 Chirality : 0.041 0.319 2461 Planarity : 0.006 0.057 2668 Dihedral : 6.742 53.081 2045 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.17 % Allowed : 33.90 % Favored : 60.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.19), residues: 1840 helix: 3.57 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.75 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 61 TYR 0.024 0.002 TYR T 50 PHE 0.004 0.001 PHE Q 19 TRP 0.011 0.002 TRP M 10 Details of bonding type rmsd covalent geometry : bond 0.00398 (15019) covalent geometry : angle 0.79797 (20470) hydrogen bonds : bond 0.05024 ( 1288) hydrogen bonds : angle 3.71238 ( 3864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 960 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9064 (mt0) cc_final: 0.8737 (mt0) REVERT: A 56 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8177 (mm-30) REVERT: A 60 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.8411 (t80) REVERT: B 27 GLN cc_start: 0.9090 (mt0) cc_final: 0.8800 (mt0) REVERT: B 45 GLN cc_start: 0.8857 (tp40) cc_final: 0.8627 (tp40) REVERT: C 21 ASP cc_start: 0.8465 (m-30) cc_final: 0.8049 (m-30) REVERT: C 23 THR cc_start: 0.9143 (m) cc_final: 0.8197 (p) REVERT: C 27 GLN cc_start: 0.8943 (mt0) cc_final: 0.8514 (mp10) REVERT: C 56 GLU cc_start: 0.8815 (tt0) cc_final: 0.8521 (mm-30) REVERT: C 60 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7581 (t80) REVERT: D 27 GLN cc_start: 0.8821 (mt0) cc_final: 0.8405 (mt0) REVERT: D 42 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8131 (m) REVERT: E 42 SER cc_start: 0.9258 (m) cc_final: 0.8163 (m) REVERT: E 67 THR cc_start: 0.9407 (t) cc_final: 0.9124 (p) REVERT: F 45 GLN cc_start: 0.8733 (tp40) cc_final: 0.7920 (tm-30) REVERT: G 45 GLN cc_start: 0.8658 (tp40) cc_final: 0.7971 (tm-30) REVERT: G 49 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7605 (mt-10) REVERT: G 56 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8270 (mm-30) REVERT: G 59 LEU cc_start: 0.9394 (mm) cc_final: 0.9163 (mt) REVERT: G 72 LYS cc_start: 0.9003 (ttpt) cc_final: 0.7882 (ttmt) REVERT: H 14 SER cc_start: 0.9160 (t) cc_final: 0.8791 (p) REVERT: H 20 ASP cc_start: 0.9028 (m-30) cc_final: 0.8666 (m-30) REVERT: H 56 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8548 (mm-30) REVERT: H 72 LYS cc_start: 0.8899 (ttpt) cc_final: 0.7861 (ttmt) REVERT: I 20 ASP cc_start: 0.8912 (m-30) cc_final: 0.8654 (m-30) REVERT: I 23 THR cc_start: 0.9128 (m) cc_final: 0.8845 (p) REVERT: I 56 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8498 (mm-30) REVERT: I 60 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8019 (t80) REVERT: I 72 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8046 (ttmt) REVERT: J 39 LYS cc_start: 0.9307 (mmtt) cc_final: 0.8954 (mmmt) REVERT: J 56 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8439 (mt-10) REVERT: J 72 LYS cc_start: 0.8897 (ttpt) cc_final: 0.7835 (ttmt) REVERT: K 21 ASP cc_start: 0.8487 (m-30) cc_final: 0.8169 (m-30) REVERT: K 56 GLU cc_start: 0.8927 (tt0) cc_final: 0.8568 (mt-10) REVERT: K 72 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8014 (ttmt) REVERT: L 27 GLN cc_start: 0.9176 (mt0) cc_final: 0.8723 (mt0) REVERT: L 40 ASN cc_start: 0.8638 (p0) cc_final: 0.8374 (p0) REVERT: L 45 GLN cc_start: 0.8482 (tp40) cc_final: 0.8143 (tp40) REVERT: L 60 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7681 (t80) REVERT: L 72 LYS cc_start: 0.8758 (ttpt) cc_final: 0.7696 (ttmt) REVERT: M 21 ASP cc_start: 0.8613 (m-30) cc_final: 0.8360 (m-30) REVERT: M 27 GLN cc_start: 0.9048 (mt0) cc_final: 0.8414 (mp10) REVERT: M 56 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8419 (mm-30) REVERT: N 10 TRP cc_start: 0.8691 (p-90) cc_final: 0.7907 (p-90) REVERT: N 20 ASP cc_start: 0.9054 (m-30) cc_final: 0.8693 (m-30) REVERT: N 45 GLN cc_start: 0.8532 (tp40) cc_final: 0.8205 (tm-30) REVERT: N 56 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8101 (mm-30) REVERT: O 10 TRP cc_start: 0.8757 (p-90) cc_final: 0.8352 (p-90) REVERT: O 21 ASP cc_start: 0.8536 (m-30) cc_final: 0.7899 (m-30) REVERT: O 23 THR cc_start: 0.9172 (m) cc_final: 0.8760 (p) REVERT: O 24 GLN cc_start: 0.8811 (pm20) cc_final: 0.8464 (pm20) REVERT: O 45 GLN cc_start: 0.8532 (tp40) cc_final: 0.7841 (tm-30) REVERT: O 49 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7424 (mt-10) REVERT: O 56 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8409 (mm-30) REVERT: P 35 ASP cc_start: 0.8869 (m-30) cc_final: 0.8550 (m-30) REVERT: P 56 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8088 (mm-30) REVERT: P 80 GLN cc_start: 0.8967 (tp40) cc_final: 0.8615 (tp-100) REVERT: Q 24 GLN cc_start: 0.8544 (pm20) cc_final: 0.8161 (pm20) REVERT: Q 35 ASP cc_start: 0.8876 (m-30) cc_final: 0.8477 (m-30) REVERT: Q 45 GLN cc_start: 0.8122 (tp40) cc_final: 0.7626 (tm-30) REVERT: R 60 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8511 (t80) REVERT: R 66 ASN cc_start: 0.8859 (m-40) cc_final: 0.8564 (m-40) REVERT: R 80 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8465 (tp-100) REVERT: S 27 GLN cc_start: 0.8725 (mt0) cc_final: 0.8164 (tm-30) REVERT: S 56 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: S 69 LYS cc_start: 0.8641 (tptp) cc_final: 0.7516 (mttm) REVERT: T 27 GLN cc_start: 0.8626 (mt0) cc_final: 0.8090 (tm-30) REVERT: T 45 GLN cc_start: 0.8379 (tp40) cc_final: 0.8059 (tm-30) REVERT: T 69 LYS cc_start: 0.8462 (tptp) cc_final: 0.7356 (mttt) REVERT: U 23 THR cc_start: 0.9229 (m) cc_final: 0.8624 (p) REVERT: U 27 GLN cc_start: 0.8723 (mt0) cc_final: 0.8224 (tm-30) REVERT: U 45 GLN cc_start: 0.8817 (tp40) cc_final: 0.8376 (tm-30) REVERT: U 61 ARG cc_start: 0.8897 (mmt180) cc_final: 0.8673 (mmt-90) REVERT: U 69 LYS cc_start: 0.8532 (tptp) cc_final: 0.7275 (mttt) REVERT: V 14 SER cc_start: 0.9112 (t) cc_final: 0.8605 (p) REVERT: V 21 ASP cc_start: 0.8579 (m-30) cc_final: 0.8283 (m-30) REVERT: V 60 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8276 (t80) REVERT: W 10 TRP cc_start: 0.8829 (p-90) cc_final: 0.8123 (p-90) REVERT: W 23 THR cc_start: 0.9251 (m) cc_final: 0.8876 (p) REVERT: W 45 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8101 (tm-30) REVERT: W 69 LYS cc_start: 0.8705 (tptp) cc_final: 0.8007 (ttmt) outliers start: 88 outliers final: 72 residues processed: 1001 average time/residue: 0.0976 time to fit residues: 151.6727 Evaluate side-chains 1037 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 957 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN E 40 ASN F 40 ASN F 64 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN P 40 ASN Q 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079534 restraints weight = 26936.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082978 restraints weight = 12897.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.085509 restraints weight = 7801.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087221 restraints weight = 5326.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088522 restraints weight = 3995.622| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15019 Z= 0.175 Angle : 0.818 13.723 20470 Z= 0.413 Chirality : 0.042 0.336 2461 Planarity : 0.006 0.058 2668 Dihedral : 6.744 52.751 2045 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.23 % Allowed : 33.55 % Favored : 61.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.19), residues: 1840 helix: 3.52 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.72 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 61 TYR 0.024 0.002 TYR T 50 PHE 0.004 0.001 PHE M 19 TRP 0.020 0.002 TRP M 10 Details of bonding type rmsd covalent geometry : bond 0.00409 (15019) covalent geometry : angle 0.81796 (20470) hydrogen bonds : bond 0.05044 ( 1288) hydrogen bonds : angle 3.72061 ( 3864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 961 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.9096 (mt0) cc_final: 0.8725 (mt0) REVERT: A 56 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8190 (mm-30) REVERT: A 60 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8400 (t80) REVERT: B 45 GLN cc_start: 0.8852 (tp40) cc_final: 0.8617 (tp40) REVERT: C 21 ASP cc_start: 0.8476 (m-30) cc_final: 0.8070 (m-30) REVERT: C 23 THR cc_start: 0.9141 (m) cc_final: 0.8197 (p) REVERT: C 27 GLN cc_start: 0.8943 (mt0) cc_final: 0.8515 (mp10) REVERT: C 56 GLU cc_start: 0.8825 (tt0) cc_final: 0.8509 (mm-30) REVERT: C 60 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7568 (t80) REVERT: D 42 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8012 (m) REVERT: E 42 SER cc_start: 0.9281 (m) cc_final: 0.8175 (m) REVERT: E 67 THR cc_start: 0.9406 (t) cc_final: 0.9116 (p) REVERT: F 45 GLN cc_start: 0.8722 (tp40) cc_final: 0.7919 (tm-30) REVERT: G 45 GLN cc_start: 0.8675 (tp40) cc_final: 0.7649 (tm-30) REVERT: G 49 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7606 (mt-10) REVERT: G 56 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8262 (mm-30) REVERT: G 59 LEU cc_start: 0.9357 (mm) cc_final: 0.9120 (mt) REVERT: G 72 LYS cc_start: 0.9007 (ttpt) cc_final: 0.7881 (ttmt) REVERT: H 20 ASP cc_start: 0.9004 (m-30) cc_final: 0.8627 (m-30) REVERT: H 23 THR cc_start: 0.9183 (m) cc_final: 0.8774 (p) REVERT: H 56 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8565 (mm-30) REVERT: H 72 LYS cc_start: 0.8891 (ttpt) cc_final: 0.7847 (ttmt) REVERT: I 20 ASP cc_start: 0.8903 (m-30) cc_final: 0.8664 (m-30) REVERT: I 23 THR cc_start: 0.9118 (m) cc_final: 0.8795 (p) REVERT: I 45 GLN cc_start: 0.8553 (tm-30) cc_final: 0.7921 (tm-30) REVERT: I 56 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8497 (mm-30) REVERT: I 60 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8005 (t80) REVERT: I 72 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8047 (ttmt) REVERT: J 39 LYS cc_start: 0.9302 (mmtt) cc_final: 0.8950 (mmmt) REVERT: J 56 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8435 (mt-10) REVERT: J 72 LYS cc_start: 0.8896 (ttpt) cc_final: 0.7834 (ttmt) REVERT: K 21 ASP cc_start: 0.8466 (m-30) cc_final: 0.8150 (m-30) REVERT: K 56 GLU cc_start: 0.8928 (tt0) cc_final: 0.8564 (mt-10) REVERT: K 72 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8014 (ttmt) REVERT: L 40 ASN cc_start: 0.8627 (p0) cc_final: 0.8356 (p0) REVERT: L 45 GLN cc_start: 0.8527 (tp40) cc_final: 0.8112 (tp40) REVERT: L 60 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.7736 (t80) REVERT: L 72 LYS cc_start: 0.8765 (ttpt) cc_final: 0.7726 (ttmt) REVERT: M 21 ASP cc_start: 0.8609 (m-30) cc_final: 0.8349 (m-30) REVERT: M 27 GLN cc_start: 0.9060 (mt0) cc_final: 0.8463 (mp10) REVERT: M 56 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8419 (mm-30) REVERT: N 10 TRP cc_start: 0.8641 (p-90) cc_final: 0.7827 (p-90) REVERT: N 20 ASP cc_start: 0.9051 (m-30) cc_final: 0.8617 (m-30) REVERT: N 27 GLN cc_start: 0.9222 (mt0) cc_final: 0.8731 (mt0) REVERT: N 45 GLN cc_start: 0.8532 (tp40) cc_final: 0.8174 (tm-30) REVERT: N 56 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8090 (mm-30) REVERT: O 10 TRP cc_start: 0.8748 (p-90) cc_final: 0.8344 (p-90) REVERT: O 21 ASP cc_start: 0.8541 (m-30) cc_final: 0.7901 (m-30) REVERT: O 23 THR cc_start: 0.9172 (m) cc_final: 0.8777 (p) REVERT: O 24 GLN cc_start: 0.8824 (pm20) cc_final: 0.8479 (pm20) REVERT: O 45 GLN cc_start: 0.8449 (tp40) cc_final: 0.7752 (tm-30) REVERT: O 49 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7373 (mt-10) REVERT: O 56 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8415 (mm-30) REVERT: P 35 ASP cc_start: 0.8872 (m-30) cc_final: 0.8547 (m-30) REVERT: P 45 GLN cc_start: 0.8557 (tp40) cc_final: 0.8313 (tp40) REVERT: P 56 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8081 (mm-30) REVERT: P 80 GLN cc_start: 0.8984 (tp40) cc_final: 0.8626 (tp-100) REVERT: Q 24 GLN cc_start: 0.8668 (pm20) cc_final: 0.8204 (pm20) REVERT: Q 35 ASP cc_start: 0.8896 (m-30) cc_final: 0.8450 (m-30) REVERT: Q 45 GLN cc_start: 0.8059 (tp40) cc_final: 0.7617 (tm-30) REVERT: R 27 GLN cc_start: 0.9075 (mt0) cc_final: 0.8683 (mt0) REVERT: R 60 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8404 (t80) REVERT: R 66 ASN cc_start: 0.8831 (m-40) cc_final: 0.8535 (m-40) REVERT: R 80 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8461 (tp-100) REVERT: S 27 GLN cc_start: 0.8662 (mt0) cc_final: 0.8080 (tm-30) REVERT: S 56 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: S 69 LYS cc_start: 0.8638 (tptp) cc_final: 0.7502 (mttm) REVERT: T 27 GLN cc_start: 0.8611 (mt0) cc_final: 0.8078 (tm-30) REVERT: T 45 GLN cc_start: 0.8375 (tp40) cc_final: 0.8072 (tm-30) REVERT: T 69 LYS cc_start: 0.8462 (tptp) cc_final: 0.7356 (mttt) REVERT: U 23 THR cc_start: 0.9229 (m) cc_final: 0.8661 (p) REVERT: U 27 GLN cc_start: 0.8726 (mt0) cc_final: 0.8382 (tt0) REVERT: U 45 GLN cc_start: 0.8812 (tp40) cc_final: 0.8456 (tm-30) REVERT: U 61 ARG cc_start: 0.8884 (mmt180) cc_final: 0.8668 (mmt-90) REVERT: U 69 LYS cc_start: 0.8521 (tptp) cc_final: 0.7263 (mttt) REVERT: V 14 SER cc_start: 0.9101 (t) cc_final: 0.8599 (p) REVERT: V 21 ASP cc_start: 0.8555 (m-30) cc_final: 0.8266 (m-30) REVERT: V 60 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8328 (t80) REVERT: W 10 TRP cc_start: 0.8854 (p-90) cc_final: 0.8172 (p-90) REVERT: W 23 THR cc_start: 0.9307 (m) cc_final: 0.9019 (p) REVERT: W 24 GLN cc_start: 0.8690 (pm20) cc_final: 0.8384 (pm20) REVERT: W 45 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8110 (tm-30) REVERT: W 69 LYS cc_start: 0.8698 (tptp) cc_final: 0.8002 (ttmt) outliers start: 89 outliers final: 72 residues processed: 1002 average time/residue: 0.0947 time to fit residues: 147.3216 Evaluate side-chains 1035 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 955 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 78 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 26 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN D 45 GLN E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 ASN Q 40 ASN S 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.080090 restraints weight = 26827.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.083576 restraints weight = 12829.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086015 restraints weight = 7718.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087868 restraints weight = 5351.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.088826 restraints weight = 3981.093| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15019 Z= 0.174 Angle : 0.829 13.631 20470 Z= 0.416 Chirality : 0.042 0.326 2461 Planarity : 0.006 0.057 2668 Dihedral : 6.752 52.871 2045 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.17 % Allowed : 34.31 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.19), residues: 1840 helix: 3.50 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.72 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 61 TYR 0.025 0.002 TYR T 50 PHE 0.004 0.001 PHE Q 19 TRP 0.018 0.002 TRP M 10 Details of bonding type rmsd covalent geometry : bond 0.00404 (15019) covalent geometry : angle 0.82931 (20470) hydrogen bonds : bond 0.05001 ( 1288) hydrogen bonds : angle 3.71542 ( 3864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.42 seconds wall clock time: 52 minutes 48.46 seconds (3168.46 seconds total)